LongevityMap variant group

Entry Details

Longevity Association
Non-significant
Population
European
Study Design
Meta-analysis of genome-wide association studies of survival and survival free of major disease or death. In total, there were 25,007 participants over 55 years of age and followed-up for over 10 years for mortality and over 8 years for event-free survival.
Conclusions
No SNP was significantly associated with mortality after correcting for multiple testing, but 14 independent SNPs were associated with time to death at a suggestive threshold

Variants (14)

ATG4C

1.
Identifier
rs12042640
Cytogenetic Location
1p31.3
UCSC Genome Browser
View 1p31.3 on the UCSC genome browser

Gene details

HGNC symbol
ATG4C
Aliases
APG4C; AUTL1; AUTL3; APG4-C 
Common name
autophagy related 4C cysteine peptidase 
Description
Autophagy is the process by which endogenous proteins and damaged organelles are destroyed intracellularly. Autophagy is postulated to be essential for cell homeostasis and cell remodeling during differentiation, metamorphosis, non-apoptotic cell death, and aging. Reduced levels of autophagy have been described in some malignant tumors, and a role for autophagy in controlling the unregulated cell growth linked to cancer has been proposed. This gene encodes a member of the autophagin protein family. The encoded protein is also designated as a member of the C-54 family of cysteine proteases. Alternate transcriptional splice variants, encoding the same protein, have been characterized. [provided by RefSeq, Jul 2008]
OMIM
611339
Ensembl
ENSG00000125703
UniProt/Swiss-Prot
ATG4C_HUMAN
Entrez Gene
84938
UniGene
7353
HapMap
View on HapMap

Homologs in model organisms

Caenorhabditis elegans
atg-4.2
Danio rerio
atg4c
Drosophila melanogaster
Atg4b
Mus musculus
Atg4c
Rattus norvegicus
Atg4c
Saccharomyces cerevisiae
ATG4
Schizosaccharomyces pombe
atg4

In other databases

GenAge model organism genes
  • A homolog of this gene for Caenorhabditis elegans is present as atg-4.2

BIN2

1.
Identifier
rs766903
Cytogenetic Location
12q13.13
UCSC Genome Browser
View 12q13.13 on the UCSC genome browser

Gene details

HGNC symbol
BIN2
Aliases
BRAP-1 
Common name
bridging integrator 2 
Description
OMIM
605936
Ensembl
ENSG00000110934
UniProt/Swiss-Prot
A0A087X188_HUMAN
Entrez Gene
51411
UniGene
14770
HapMap
View on HapMap

Homologs in model organisms

Caenorhabditis elegans
amph-1
Danio rerio
bin2b
Drosophila melanogaster
Amph
Mus musculus
Bin2
Rattus norvegicus
Bin2

COL5A1

1.
Identifier
rs3128591
Cytogenetic Location
9q34.3
UCSC Genome Browser
View 9q34.3 on the UCSC genome browser

Gene details

HGNC symbol
COL5A1
Aliases
EDSC 
Common name
collagen type V alpha 1 chain 
Description
This gene encodes an alpha chain for one of the low abundance fibrillar collagens. Fibrillar collagen molecules are trimers that can be composed of one or more types of alpha chains. Type V collagen is found in tissues containing type I collagen and appears to regulate the assembly of heterotypic fibers composed of both type I and type V collagen. This gene product is closely related to type XI collagen and it is possible that the collagen chains of types V and XI constitute a single collagen type with tissue-specific chain combinations. The encoded procollagen protein occurs commonly as the heterotrimer pro-alpha1(V)-pro-alpha1(V)-pro-alpha2(V). Mutations in this gene are associated with Ehlers-Danlos syndrome, types I and II. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2013]
OMIM
120215
Ensembl
ENSG00000130635
UniProt/Swiss-Prot
A0A024R8E5_HUMAN
Entrez Gene
1289
UniGene
210283
HapMap
View on HapMap

Homologs in model organisms

Danio rerio
col5a1
Mus musculus
Col5a1
Rattus norvegicus
Col5a1

GRAMD1B

1.
Identifier
rs1274214
Cytogenetic Location
11q24.1
UCSC Genome Browser
View 11q24.1 on the UCSC genome browser

Gene details

HGNC symbol
GRAMD1B
Aliases
 
Common name
GRAM domain containing 1B 
Description
OMIM
Ensembl
ENSG00000023171
UniProt/Swiss-Prot
A0A024R3M2_HUMAN
Entrez Gene
57476
UniGene
144725
HapMap
View on HapMap

Homologs in model organisms

Danio rerio
gramd1ba
Danio rerio
GRAMD1B (1 of many)
Drosophila melanogaster
CG34394
Mus musculus
Gramd1b
Rattus norvegicus
Gramd1b
Saccharomyces cerevisiae
856480
Saccharomyces cerevisiae
850501
Saccharomyces cerevisiae
850761
Saccharomyces cerevisiae
YSP2

HECW2

1.
Identifier
rs4850695
Cytogenetic Location
2q32.3
UCSC Genome Browser
View 2q32.3 on the UCSC genome browser

Gene details

HGNC symbol
HECW2
Aliases
NEDL2; NDHSAL 
Common name
HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2 
Description
This gene encodes a member of a family of E3 ubiquitin ligases which plays an important role in the proliferation, migration and differentiation of neural crest cells as a regulator of glial cell line-derived neurotrophic factor (GDNF)/Ret signaling. This gene also plays an important role in angiogenesis through stabilization of endothelial cell-to-cell junctions as a regulator of angiomotin-like 1 stability. The encoded protein contains an N-terminal calcium/lipid-binding (C2) domain involved in membrane targeting, two-four WW domains responsible for cellular localization and substrate recognition, and a C-terminal homologous with E6-associated protein C-terminus (HECT) catalytic domain. Naturally occurring mutations in this gene are associated with neurodevelopmental delay, hypotonia, and epilepsy. The decreased expression of this gene in the aganglionic colon is associated with Hirschsprung's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]
OMIM
617245
Ensembl
ENSG00000138411
UniProt/Swiss-Prot
HECW2_HUMAN
Entrez Gene
57520
UniGene
633212
HapMap
View on HapMap

Homologs in model organisms

Caenorhabditis elegans
hecw-1
Danio rerio
hecw2a
Danio rerio
hecw2b
Drosophila melanogaster
CG42797
Mus musculus
Hecw2
Rattus norvegicus
Hecw2
Saccharomyces cerevisiae
RSP5

HIP1

1.
Identifier
rs17149227
Cytogenetic Location
7q11.23
UCSC Genome Browser
View 7q11.23 on the UCSC genome browser

Gene details

HGNC symbol
HIP1
Aliases
SHON; HIP-I; ILWEQ; SHONbeta; SHONgamma 
Common name
huntingtin interacting protein 1 
Description
The product of this gene is a membrane-associated protein that functions in clathrin-mediated endocytosis and protein trafficking within the cell. The encoded protein binds to the huntingtin protein in the brain; this interaction is lost in Huntington's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
OMIM
601767
Ensembl
ENSG00000127946
UniProt/Swiss-Prot
B4DK46_HUMAN
Entrez Gene
3092
UniGene
329266
HapMap
View on HapMap

Homologs in model organisms

Caenorhabditis elegans
tag-138
Caenorhabditis elegans
Y18D10A.22
Caenorhabditis elegans
hipr-1
Danio rerio
hip1
Drosophila melanogaster
Hip1
Mus musculus
Hip1
Rattus norvegicus
Hip1
Saccharomyces cerevisiae
SLA2
Schizosaccharomyces pombe
end4

KCNQ4

1.
Identifier
rs2769255
Cytogenetic Location
1p34.2
UCSC Genome Browser
View 1p34.2 on the UCSC genome browser

Gene details

HGNC symbol
KCNQ4
Aliases
DFNA2; KV7.4; DFNA2A 
Common name
potassium voltage-gated channel subfamily Q member 4 
Description
The protein encoded by this gene forms a potassium channel that is thought to play a critical role in the regulation of neuronal excitability, particularly in sensory cells of the cochlea. The current generated by this channel is inhibited by M1 muscarinic acetylcholine receptors and activated by retigabine, a novel anti-convulsant drug. The encoded protein can form a homomultimeric potassium channel or possibly a heteromultimeric channel in association with the protein encoded by the KCNQ3 gene. Defects in this gene are a cause of nonsyndromic sensorineural deafness type 2 (DFNA2), an autosomal dominant form of progressive hearing loss. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
OMIM
603537
Ensembl
ENSG00000117013
UniProt/Swiss-Prot
B3KQH8_HUMAN
Entrez Gene
9132
UniGene
473058
HapMap
View on HapMap

Homologs in model organisms

Caenorhabditis elegans
kqt-1
Danio rerio
kcnq4
Drosophila melanogaster
KCNQ
Mus musculus
Kcnq4
Rattus norvegicus
Kcnq4

LMO4

1.
Identifier
rs11582903
Cytogenetic Location
1p22.3
UCSC Genome Browser
View 1p22.3 on the UCSC genome browser

Gene details

HGNC symbol
LMO4
Aliases
 
Common name
LIM domain only 4 
Description
This gene encodes a cysteine-rich protein that contains two LIM domains but lacks a DNA-binding homeodomain. The encoded protein may play a role as a transcriptional regulator or as an oncogene. [provided by RefSeq, Aug 2008]
OMIM
603129
Ensembl
ENSG00000143013
UniProt/Swiss-Prot
LMO4_HUMAN
Entrez Gene
8543
UniGene
436792
HapMap
View on HapMap

Homologs in model organisms

Danio rerio
lmo4b
Drosophila melanogaster
CG5708
Mus musculus
Lmo4
Rattus norvegicus
Lmo4

LOC107987043

1.
Identifier
rs10811679
Cytogenetic Location
9p24.3-p24.2
UCSC Genome Browser
View 9p24.3-p24.2 on the UCSC genome browser

Gene details

HGNC symbol
LOC107987043
Aliases
 
Common name
uncharacterized LOC107987043 
Description
OMIM
Ensembl
UniProt/Swiss-Prot
Entrez Gene
107987043
UniGene
HapMap
View on HapMap

Homologs in model organisms

No homologs found

MYLK4

1.
Identifier
rs17291546
Cytogenetic Location
6p25.2
UCSC Genome Browser
View 6p25.2 on the UCSC genome browser

Gene details

HGNC symbol
MYLK4
Aliases
SgK085 
Common name
myosin light chain kinase family member 4 
Description
OMIM
Ensembl
ENSG00000145949
UniProt/Swiss-Prot
MYLK4_HUMAN
Entrez Gene
340156
UniGene
127830
HapMap
View on HapMap

Homologs in model organisms

Caenorhabditis elegans
ZC373.4
Danio rerio
mylk4a
Danio rerio
mylk4b
Mus musculus
Mylk4
Rattus norvegicus
Mylk4
Rattus norvegicus
Mylk4
Saccharomyces cerevisiae
MEK1

NETO1

1.
Identifier
rs12606100
Cytogenetic Location
18q22.3
UCSC Genome Browser
View 18q22.3 on the UCSC genome browser

Gene details

HGNC symbol
NETO1
Aliases
BCTL1; BTCL1 
Common name
neuropilin and tolloid like 1 
Description
This gene encodes a predicted transmembrane protein containing two extracellular CUB domains followed by a low-density lipoprotein class A (LDLa) domain. A similar gene in mice encodes a protein that plays a critical role in spatial learning and memory by regulating the function of synaptic N-methyl-D-aspartic acid receptor complexes in the hippocampus. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2011]
OMIM
607973
Ensembl
ENSG00000166342
UniProt/Swiss-Prot
A0A024R375_HUMAN
Entrez Gene
81832
UniGene
465407
HapMap
View on HapMap

Homologs in model organisms

Caenorhabditis elegans
neto-1
Danio rerio
neto1l
Danio rerio
neto1
Drosophila melanogaster
Neto
Mus musculus
Neto1
Rattus norvegicus
Neto1

ORC5

1.
Identifier
rs10259086
Cytogenetic Location
7q22.1-q22.2
UCSC Genome Browser
View 7q22.1-q22.2 on the UCSC genome browser

Gene details

HGNC symbol
ORC5
Aliases
ORC5L; ORC5P; ORC5T; PPP1R117 
Common name
origin recognition complex subunit 5 
Description
The origin recognition complex (ORC) is a highly conserved six subunit protein complex essential for the initiation of the DNA replication in eukaryotic cells. Studies in yeast demonstrated that ORC binds specifically to origins of replication and serves as a platform for the assembly of additional initiation factors such as Cdc6 and Mcm proteins. The protein encoded by this gene is a subunit of the ORC complex. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Oct 2010]
OMIM
602331
Ensembl
ENSG00000164815
UniProt/Swiss-Prot
A4D0P7_HUMAN
Entrez Gene
5001
UniGene
432948
HapMap
View on HapMap

Homologs in model organisms

Caenorhabditis elegans
orc-5
Danio rerio
orc5
Drosophila melanogaster
Orc5
Mus musculus
Orc5
Rattus norvegicus
Orc5
Saccharomyces cerevisiae
ORC5
Schizosaccharomyces pombe
orc5

OTOL1

1.
Identifier
rs1425609
Cytogenetic Location
3q26.1
UCSC Genome Browser
View 3q26.1 on the UCSC genome browser

Gene details

HGNC symbol
OTOL1
Aliases
C1QTNF15; C1QTNF16 
Common name
otolin 1 
Description
OMIM
Ensembl
ENSG00000182447
UniProt/Swiss-Prot
OTOL1_HUMAN
Entrez Gene
131149
UniGene
585021
HapMap
View on HapMap

Homologs in model organisms

Danio rerio
otol1b
Danio rerio
otol1a
Mus musculus
Otol1
Rattus norvegicus
Otol1

VWA5A

1.
Identifier
rs4936894
Cytogenetic Location
11q24.2
UCSC Genome Browser
View 11q24.2 on the UCSC genome browser

Gene details

HGNC symbol
VWA5A
Aliases
BCSC1; BCSC-1; LOH11CR2A 
Common name
von Willebrand factor A domain containing 5A 
Description
OMIM
602929
Ensembl
ENSG00000110002
UniProt/Swiss-Prot
A0A024R3H3_HUMAN
Entrez Gene
4013
UniGene
152944
HapMap
View on HapMap

Homologs in model organisms

Danio rerio
VWA5A (1 of many)
Danio rerio
VWA5A (1 of many)
Danio rerio
VWA5A (1 of many)
Danio rerio
VWA5A (1 of many)
Mus musculus
Vwa5a
Mus musculus
AW551984
Rattus norvegicus
LOC108348048
Rattus norvegicus
Vwa5a
Rattus norvegicus
LOC108348048
Rattus norvegicus
RGD1311744
Rattus norvegicus
Vwa5a

References

Walter et al. (2011)

Other variants which are also part of this study