LongevityMap variant group

Entry Details

Longevity Association
Non-significant
Population
Dutch
Study Design
Genome-wide association study in 403 unrelated nonagenarians from long-living families and 1670 younger controls. Strongest candidates were then investigated in a meta-analysis of 4149 nonagenarian cases and 7582 younger controls.
Conclusions
No SNP reached significance in the GWAS but 62 SNPs, many in genes, had an indicative association with survival into old age. Of these 62 SNPs then studied in the meta-analysis, 61 were not significant.

Variants (57)

No gene

1.
Identifier
rs12080088
Cytogenetic Location
2.
Identifier
rs12548929
Cytogenetic Location
3.
Identifier
rs12548622
Cytogenetic Location
4.
Identifier
rs6774262
Cytogenetic Location
5.
Identifier
rs4133282
Cytogenetic Location
6.
Identifier
rs16861446
Cytogenetic Location
7.
Identifier
rs970567
Cytogenetic Location
8.
Identifier
rs1859416
Cytogenetic Location
9.
Identifier
rs12101383
Cytogenetic Location
10.
Identifier
rs268300
Cytogenetic Location
11.
Identifier
rs10490478
Cytogenetic Location
12.
Identifier
rs2436932
Cytogenetic Location
13.
Identifier
rs11122430
Cytogenetic Location
14.
Identifier
rs9662589
Cytogenetic Location
15.
Identifier
rs10191593
Cytogenetic Location
16.
Identifier
rs6581191
Cytogenetic Location
17.
Identifier
rs6852830
Cytogenetic Location
18.
Identifier
rs6941242
Cytogenetic Location
19.
Identifier
rs9473350
Cytogenetic Location
20.
Identifier
rs17154903
Cytogenetic Location
21.
Identifier
rs4110518
Cytogenetic Location
22.
Identifier
rs1893132
Cytogenetic Location
23.
Identifier
rs7661225
Cytogenetic Location
24.
Identifier
rs11129533
Cytogenetic Location
25.
Identifier
rs7830605
Cytogenetic Location
26.
Identifier
rs2033563
Cytogenetic Location
27.
Identifier
rs13248142
Cytogenetic Location
28.
Identifier
rs625249
Cytogenetic Location
29.
Identifier
rs6577989
Cytogenetic Location
30.
Identifier
rs4736209
Cytogenetic Location
31.
Identifier
rs660100
Cytogenetic Location

ANKUB1

1.
Identifier
rs4681554
Cytogenetic Location
3q25.1
UCSC Genome Browser
View 3q25.1 on the UCSC genome browser

Gene details

HGNC symbol
ANKUB1
Aliases
C3orf16 
Common name
ankyrin repeat and ubiquitin domain containing 1 
Description
OMIM
Ensembl
ENSG00000206199
UniProt/Swiss-Prot
ANKUB_HUMAN
Entrez Gene
389161
UniGene
665988
HapMap
View on HapMap

Homologs in model organisms

Mus musculus
Ankub1
Rattus norvegicus
Ankub1

ATP5J2-PTCD1

1.
Identifier
rs2003499
Cytogenetic Location
7q22.1
UCSC Genome Browser
View 7q22.1 on the UCSC genome browser

Gene details

HGNC symbol
ATP5J2-PTCD1
Aliases
 
Common name
ATP5J2-PTCD1 readthrough 
Description
This locus represents naturally occurring read-through transcription between the ATP5J2 (ATP synthase, H+ transporting, mitochondrial Fo complex, subunit F2) and PTCD1 (pentatricopeptide repeat domain 1) genes on chromosome 7. The read-through transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Nov 2010]
OMIM
Ensembl
ENSG00000248919
UniProt/Swiss-Prot
B4DJ38_HUMAN
Entrez Gene
100526740
UniGene
632313
HapMap
View on HapMap

Homologs in model organisms

Danio rerio
ptcd1
Drosophila melanogaster
CG4611
Mus musculus
Ptcd1
Rattus norvegicus
Ptcd1

CASC21

1.
Identifier
rs11782735
Cytogenetic Location
8q24.21
UCSC Genome Browser
View 8q24.21 on the UCSC genome browser
2.
Identifier
rs11776260
Cytogenetic Location
8q24.21
UCSC Genome Browser
View 8q24.21 on the UCSC genome browser

Gene details

HGNC symbol
CASC21
Aliases
CARLo-2; LINC01244 
Common name
cancer susceptibility 21 (non-protein coding) 
Description
Other longevity studies of this gene
1
OMIM
Ensembl
UniProt/Swiss-Prot
Entrez Gene
103021164
UniGene
571531
HapMap
View on HapMap

Homologs in model organisms

No homologs found

CCDC192

1.
Identifier
rs1421746
Cytogenetic Location
5q23.2-q23.3
UCSC Genome Browser
View 5q23.2-q23.3 on the UCSC genome browser

Gene details

HGNC symbol
CCDC192
Aliases
LINC01183 
Common name
coiled-coil domain containing 192 
Description
OMIM
Ensembl
ENSG00000230561
UniProt/Swiss-Prot
CC192_HUMAN
Entrez Gene
728586
UniGene
582532
HapMap
View on HapMap

Homologs in model organisms

Mus musculus
1700011I03Rik

CCDC50

1.
Identifier
rs3959143
Cytogenetic Location
3q28
UCSC Genome Browser
View 3q28 on the UCSC genome browser
2.
Identifier
rs9827142
Cytogenetic Location
3q28
UCSC Genome Browser
View 3q28 on the UCSC genome browser
3.
Identifier
rs9868286
Cytogenetic Location
3q28
UCSC Genome Browser
View 3q28 on the UCSC genome browser

Gene details

HGNC symbol
CCDC50
Aliases
YMER; C3orf6; DFNA44 
Common name
coiled-coil domain containing 50 
Description
This gene encodes a soluble, cytoplasmic, tyrosine-phosphorylated protein with multiple ubiquitin-interacting domains. Mutations in this gene cause nonsyndromic, postlingual, progressive sensorineural DFNA44 hearing loss. In mouse, the protein is expressed in the inner ear during development and postnatal maturation and associates with microtubule-based structures. This protein may also function as a negative regulator of NF-kB signaling and as an effector of epidermal growth factor (EGF)-mediated cell signaling. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Oct 2008]
Other longevity studies of this gene
2
OMIM
611051
Ensembl
ENSG00000152492
UniProt/Swiss-Prot
CCD50_HUMAN
Entrez Gene
152137
UniGene
478682
HapMap
View on HapMap

Homologs in model organisms

Danio rerio
ccdc50
Mus musculus
Ccdc50
Rattus norvegicus
Ccdc50

DOK6

1.
Identifier
rs10401068
Cytogenetic Location
18q22.2
UCSC Genome Browser
View 18q22.2 on the UCSC genome browser

Gene details

HGNC symbol
DOK6
Aliases
DOK5L; HsT3226 
Common name
docking protein 6 
Description
DOK6 is a member of the DOK (see DOK1; MIM 602919) family of intracellular adaptors that play a role in the RET (MIM 164761) signaling cascade (Crowder et al., 2004 [PubMed 15286081]).[supplied by OMIM, Mar 2008]
OMIM
611402
Ensembl
ENSG00000206052
UniProt/Swiss-Prot
DOK6_HUMAN
Entrez Gene
220164
UniGene
278285
HapMap
View on HapMap

Homologs in model organisms

Danio rerio
dok6
Drosophila melanogaster
Dok
Mus musculus
Dok6
Rattus norvegicus
Dok6

GRWD1

1.
Identifier
rs2302951
Cytogenetic Location
19q13.33
UCSC Genome Browser
View 19q13.33 on the UCSC genome browser

Gene details

HGNC symbol
GRWD1
Aliases
CDW4; GRWD; RRB1; WDR28 
Common name
glutamate rich WD repeat containing 1 
Description
This gene encodes a glutamate-rich protein that contains five WD-repeat motifs. The encoded protein may play a critical role in ribosome biogenesis and may also play a role in histone methylation through interactions with CUL4-DDB1 ubiquitin E3 ligase. [provided by RefSeq, Feb 2012]
OMIM
610597
Ensembl
ENSG00000105447
UniProt/Swiss-Prot
GRWD1_HUMAN
Entrez Gene
83743
UniGene
400625
HapMap
View on HapMap

Homologs in model organisms

Caenorhabditis elegans
Y54H5A.1
Danio rerio
grwd1
Drosophila melanogaster
l(2)09851
Mus musculus
Grwd1
Rattus norvegicus
Grwd1
Saccharomyces cerevisiae
RRB1
Schizosaccharomyces pombe
rrb1

HECW1

1.
Identifier
rs886550
Cytogenetic Location
7p14.1-p13
UCSC Genome Browser
View 7p14.1-p13 on the UCSC genome browser

Gene details

HGNC symbol
HECW1
Aliases
NEDL1 
Common name
HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 
Description
OMIM
610384
Ensembl
ENSG00000002746
UniProt/Swiss-Prot
HECW1_HUMAN
Entrez Gene
23072
UniGene
164453
HapMap
View on HapMap

Homologs in model organisms

Caenorhabditis elegans
hecw-1
Danio rerio
si:ch211-188f17.1
Drosophila melanogaster
CG42797
Mus musculus
Hecw1
Rattus norvegicus
Hecw1
Saccharomyces cerevisiae
RSP5

KCNMA1

1.
Identifier
rs1516507
Cytogenetic Location
10q22.3
UCSC Genome Browser
View 10q22.3 on the UCSC genome browser

Gene details

HGNC symbol
KCNMA1
Aliases
SLO; BKTM; SLO1; hSlo; MaxiK; SAKCA; mSLO1; KCa1.1; SLO-ALPHA; bA205K10.1 
Common name
potassium calcium-activated channel subfamily M alpha 1 
Description
MaxiK channels are large conductance, voltage and calcium-sensitive potassium channels which are fundamental to the control of smooth muscle tone and neuronal excitability. MaxiK channels can be formed by 2 subunits: the pore-forming alpha subunit, which is the product of this gene, and the modulatory beta subunit. Intracellular calcium regulates the physical association between the alpha and beta subunits. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
OMIM
600150
Ensembl
ENSG00000156113
UniProt/Swiss-Prot
A0A087WZL8_HUMAN
Entrez Gene
3778
UniGene
144795
HapMap
View on HapMap

Homologs in model organisms

Caenorhabditis elegans
slo-1
Danio rerio
kcnma1a
Drosophila melanogaster
slo
Mus musculus
Kcnma1
Rattus norvegicus
Kcnma1

LOC101927245

1.
Identifier
rs2511703
Cytogenetic Location
8q22.3
UCSC Genome Browser
View 8q22.3 on the UCSC genome browser

Gene details

HGNC symbol
LOC101927245
Aliases
 
Common name
vegetative cell wall protein gp1-like 
Description
OMIM
Ensembl
UniProt/Swiss-Prot
Entrez Gene
101927245
UniGene
HapMap
View on HapMap

Homologs in model organisms

No homologs found

LRP1B

1.
Identifier
rs10194564
Cytogenetic Location
2q22.1-q22.2
UCSC Genome Browser
View 2q22.1-q22.2 on the UCSC genome browser

Gene details

HGNC symbol
LRP1B
Aliases
LRP-1B; LRPDIT; LRP-DIT 
Common name
LDL receptor related protein 1B 
Description
This gene encodes a member of the low density lipoprotein (LDL) receptor family. These receptors play a wide variety of roles in normal cell function and development due to their interactions with multiple ligands. Disruption of this gene has been reported in several types of cancer. [provided by RefSeq, Jun 2016]
Other longevity studies of this gene
1
OMIM
608766
Ensembl
ENSG00000168702
UniProt/Swiss-Prot
LRP1B_HUMAN
Entrez Gene
53353
UniGene
656461
HapMap
View on HapMap

Homologs in model organisms

Caenorhabditis elegans
F14B4.1
Danio rerio
lrp1ba
Drosophila melanogaster
LRP1
Mus musculus
Lrp1b
Rattus norvegicus
Lrp1b

MMP20

1.
Identifier
rs10502005
Cytogenetic Location
11q22.2
UCSC Genome Browser
View 11q22.2 on the UCSC genome browser

Gene details

HGNC symbol
MMP20
Aliases
AI2A2; MMP-20 
Common name
matrix metallopeptidase 20 
Description
Proteins of the matrix metalloproteinase (MMP) family are involved in the breakdown of extracellular matrix in normal physiological processes, such as embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. Most MMP's are secreted as inactive proproteins which are activated when cleaved by extracellular proteinases. The protein encoded by this gene degrades amelogenin, the major protein component of dental enamel matrix, and thus thought to play a role in tooth enamel formation. A mutation in this gene, which alters the normal splice pattern and results in premature termination of the encoded protein, has been associated with amelogenesis imperfecta. This gene is part of a cluster of MMP genes located on chromosome 11q22.3. [provided by RefSeq, Aug 2011]
OMIM
604629
Ensembl
ENSG00000137674
UniProt/Swiss-Prot
MMP20_HUMAN
Entrez Gene
9313
UniGene
591946
HapMap
View on HapMap

Homologs in model organisms

Danio rerio
mmp20b
Danio rerio
mmp20a
Drosophila melanogaster
Mmp2
Mus musculus
Mmp20
Rattus norvegicus
Mmp20

MRPL37

1.
Identifier
rs642990
Cytogenetic Location
1p32.3
UCSC Genome Browser
View 1p32.3 on the UCSC genome browser

Gene details

HGNC symbol
MRPL37
Aliases
L2mt; L37mt; MRPL2; RPML2; MRP-L2; MRP-L37 
Common name
mitochondrial ribosomal protein L37 
Description
Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 39S subunit protein. [provided by RefSeq, Jul 2008]
OMIM
611843
Ensembl
ENSG00000116221
UniProt/Swiss-Prot
RM37_HUMAN
Entrez Gene
51253
UniGene
584908
HapMap
View on HapMap

Homologs in model organisms

Danio rerio
mrpl37
Drosophila melanogaster
mRpL37
Mus musculus
Mrpl37
Rattus norvegicus
Mrpl37

NRXN3

1.
Identifier
rs12892152
Cytogenetic Location
14q24.3-q31.1
UCSC Genome Browser
View 14q24.3-q31.1 on the UCSC genome browser

Gene details

HGNC symbol
NRXN3
Aliases
C14orf60 
Common name
neurexin 3 
Description
This gene encodes a member of a family of proteins that function in the nervous system as receptors and cell adhesion molecules. Extensive alternative splicing and the use of alternative promoters results in multiple transcript variants and protein isoforms for this gene, but the full-length nature of many of these variants has not been determined. Transcripts that initiate from an upstream promoter encode alpha isoforms, which contain epidermal growth factor-like (EGF-like) sequences and laminin G domains. Transcripts initiating from the downstream promoter encode beta isoforms, which lack EGF-like sequences. Genetic variation at this locus has been associated with a range of behavioral phenotypes, including alcohol dependence and autism spectrum disorder. [provided by RefSeq, Dec 2012]
OMIM
600567
Ensembl
ENSG00000021645
UniProt/Swiss-Prot
A0A0U1RRJ0_HUMAN
Entrez Gene
9369
UniGene
368307
HapMap
View on HapMap

Homologs in model organisms

Caenorhabditis elegans
nrx-1
Danio rerio
nrxn3a
Danio rerio
nrxn3b
Drosophila melanogaster
Nrx-1
Mus musculus
Nrxn3

In other databases

GenAge model organism genes
  • A homolog of this gene for Caenorhabditis elegans is present as nrx-1

OR6N1

1.
Identifier
rs857785
Cytogenetic Location
1q23.1
UCSC Genome Browser
View 1q23.1 on the UCSC genome browser
2.
Identifier
rs857788
Cytogenetic Location
1q23.1
UCSC Genome Browser
View 1q23.1 on the UCSC genome browser

Gene details

HGNC symbol
OR6N1
Aliases
OR1-22 
Common name
olfactory receptor family 6 subfamily N member 1 
Description
Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]
Other longevity studies of this gene
1
OMIM
Ensembl
ENSG00000197403
UniProt/Swiss-Prot
OR6N1_HUMAN
Entrez Gene
128372
UniGene
553592
HapMap
View on HapMap

Homologs in model organisms

Mus musculus
Olfr429
Rattus norvegicus
Olr1589

PEBP4

1.
Identifier
rs7005993
Cytogenetic Location
8p21.3
UCSC Genome Browser
View 8p21.3 on the UCSC genome browser

Gene details

HGNC symbol
PEBP4
Aliases
CORK1; CORK-1; PEBP-4; hPEBP4; PRO4408; GWTM1933; HEL-S-300 
Common name
phosphatidylethanolamine binding protein 4 
Description
The phosphatidylethanolamine (PE)-binding proteins, including PEBP4, are an evolutionarily conserved family of proteins with pivotal biologic functions, such as lipid binding and inhibition of serine proteases (Wang et al., 2004 [PubMed 15302887]).[supplied by OMIM, Dec 2008]
OMIM
612473
Ensembl
ENSG00000134020
UniProt/Swiss-Prot
PEBP4_HUMAN
Entrez Gene
157310
UniGene
491242
HapMap
View on HapMap

Homologs in model organisms

Caenorhabditis elegans
F40A3.3
Caenorhabditis elegans
Y69E1A.5
Drosophila melanogaster
a5
Drosophila melanogaster
CG30060
Drosophila melanogaster
CG7054
Drosophila melanogaster
Pebp1
Drosophila melanogaster
CG6180
Drosophila melanogaster
CG17919
Drosophila melanogaster
CG17917
Drosophila melanogaster
CG10298
Mus musculus
Pebp4
Saccharomyces cerevisiae
850876
Saccharomyces cerevisiae
TFS1

RBPMS

1.
Identifier
rs7011660
Cytogenetic Location
8p12
UCSC Genome Browser
View 8p12 on the UCSC genome browser

Gene details

HGNC symbol
RBPMS
Aliases
HERMES 
Common name
RNA binding protein with multiple splicing 
Description
This gene encodes a member of the RNA recognition motif family of RNA-binding proteins. The RNA recognition motif is between 80-100 amino acids in length and family members contain one to four copies of the motif. The RNA recognition motif consists of two short stretches of conserved sequence, as well as a few highly conserved hydrophobic residues. The encoded protein has a single, putative RNA recognition motif in its N-terminus. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jun 2013]
OMIM
601558
Ensembl
ENSG00000157110
UniProt/Swiss-Prot
B4E3T4_HUMAN
Entrez Gene
11030
UniGene
334587
HapMap
View on HapMap

Homologs in model organisms

Caenorhabditis elegans
mec-8
Danio rerio
RBPMS
Drosophila melanogaster
cpo
Mus musculus
Rbpms
Rattus norvegicus
Rbpms

In other databases

GenAge model organism genes
  • A homolog of this gene for Caenorhabditis elegans is present as mec-8

SLC39A10

1.
Identifier
rs10931700
Cytogenetic Location
2q32.3
UCSC Genome Browser
View 2q32.3 on the UCSC genome browser

Gene details

HGNC symbol
SLC39A10
Aliases
LZT-Hs2 
Common name
solute carrier family 39 member 10 
Description
Zinc is an essential cofactor for hundreds of enzymes. It is involved in protein, nucleic acid, carbohydrate, and lipid metabolism, as well as in the control of gene transcription, growth, development, and differentiation. SLC39A10 belongs to a subfamily of proteins that show structural characteristics of zinc transporters (Taylor and Nicholson, 2003 [PubMed 12659941]).[supplied by OMIM, Mar 2008]
OMIM
608733
Ensembl
ENSG00000196950
UniProt/Swiss-Prot
A0A024R3W5_HUMAN
Entrez Gene
57181
UniGene
650158
HapMap
View on HapMap

Homologs in model organisms

Danio rerio
slc39a10
Drosophila melanogaster
foi
Mus musculus
Slc39a10
Rattus norvegicus
Slc39a10
Saccharomyces cerevisiae
YKE4

SOX5

1.
Identifier
rs11047358
Cytogenetic Location
12p12.1
UCSC Genome Browser
View 12p12.1 on the UCSC genome browser

Gene details

HGNC symbol
SOX5
Aliases
L-SOX5; LAMSHF; L-SOX5B; L-SOX5F 
Common name
SRY-box 5 
Description
This gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. The encoded protein may play a role in chondrogenesis. A pseudogene of this gene is located on chromosome 8. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
OMIM
604975
Ensembl
ENSG00000134532
UniProt/Swiss-Prot
A0A024RB06_HUMAN
Entrez Gene
6660
UniGene
434948
HapMap
View on HapMap

Homologs in model organisms

Danio rerio
sox5
Drosophila melanogaster
Sox102F
Mus musculus
Sox5
Rattus norvegicus
Sox5

In other databases

CellAge
  • This gene is present as SOX5

SYK

1.
Identifier
rs2290889
Cytogenetic Location
9q22.2
UCSC Genome Browser
View 9q22.2 on the UCSC genome browser
2.
Identifier
rs7864625
Cytogenetic Location
9q22.2
UCSC Genome Browser
View 9q22.2 on the UCSC genome browser

Gene details

HGNC symbol
SYK
Aliases
p72-Syk 
Common name
spleen associated tyrosine kinase 
Description
This gene encodes a member of the family of non-receptor type Tyr protein kinases. This protein is widely expressed in hematopoietic cells and is involved in coupling activated immunoreceptors to downstream signaling events that mediate diverse cellular responses, including proliferation, differentiation, and phagocytosis. It is thought to be a modulator of epithelial cell growth and a potential tumour suppressor in human breast carcinomas. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]
Other longevity studies of this gene
1
OMIM
600085
Ensembl
ENSG00000165025
UniProt/Swiss-Prot
A0A024R244_HUMAN
Entrez Gene
6850
UniGene
371720
HapMap
View on HapMap

Homologs in model organisms

Danio rerio
syk
Drosophila melanogaster
shark
Mus musculus
Syk
Rattus norvegicus
Syk

In other databases

CellAge
  • This gene is present as SYK

TTC41P

1.
Identifier
rs12815289
Cytogenetic Location
12q23.3
UCSC Genome Browser
View 12q23.3 on the UCSC genome browser

Gene details

HGNC symbol
TTC41P
Aliases
GNN; GNNP 
Common name
tetratricopeptide repeat domain 41, pseudogene 
Description
OMIM
Ensembl
ENSG00000214198
UniProt/Swiss-Prot
Entrez Gene
253724
UniGene
506549
HapMap
View on HapMap

Homologs in model organisms

No homologs found

References

Deelen et al. (2011)

Other variants which are also part of this study