COL6A5
gene geneOn this page
Also known as FLJ35880VWA4
Summary
COL6A5 (collagen type VI alpha 5 chain, HGNC:26674) is a protein-coding gene on chromosome 3q22.1, encoding Collagen alpha-5(VI) chain (A8TX70). Collagen VI acts as a cell-binding protein.
This gene encodes a member of the collagen superfamily of proteins. The encoded protein contains multiple von Willebrand factor A-like domains and may interact with the alpha 1 and alpha 2 chains of collagen VI to form the complete collagen VI trimer. Polymorphisms in this gene may be linked to dermal phenotypes, such as eczema. Alternative splicing results in multiple transcript variants.
Source: NCBI Gene 256076 — RefSeq curated summary.
At a glance
- GWAS associations: 7
- Clinical variants (ClinVar): 406 total
- Druggable target: yes
- Dosage sensitivity (ClinGen): haploinsufficiency dosage sensitivity unlikely, triplosensitivity no evidence
- MANE Select transcript:
NM_001278298
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:26674 |
| Approved symbol | COL6A5 |
| Name | collagen type VI alpha 5 chain |
| Location | 3q22.1 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | FLJ35880, VWA4 |
| Ensembl gene | ENSG00000172752 |
| Ensembl biotype | protein_coding |
| OMIM | 611916 |
| Entrez | 256076 |
Gene structure
Transcript identifiers
Ensembl transcripts: 4 — 3 protein_coding, 1 nonsense_mediated_decay
ENST00000312481, ENST00000373157, ENST00000512482, ENST00000512836
RefSeq mRNA: 3 — MANE Select: NM_001278298
NM_001278298, NM_001412157, NM_153264
CCDS: CCDS93384, CCDS93385
Canonical transcript exons
ENST00000373157 — 41 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001194266 | 130470871 | 130470967 |
| ENSE00001194273 | 130468795 | 130469481 |
| ENSE00001194278 | 130455455 | 130455666 |
| ENSE00001194287 | 130443476 | 130443566 |
| ENSE00001379257 | 130440166 | 130440825 |
| ENSE00001531459 | 130439522 | 130439615 |
| ENSE00001531461 | 130431465 | 130431949 |
| ENSE00001547997 | 130421325 | 130421360 |
| ENSE00001548142 | 130409326 | 130409388 |
| ENSE00001548940 | 130405993 | 130406019 |
| ENSE00001551288 | 130401031 | 130401173 |
| ENSE00001552037 | 130415645 | 130415707 |
| ENSE00001552649 | 130398030 | 130398111 |
| ENSE00001553178 | 130410009 | 130410074 |
| ENSE00001553245 | 130416757 | 130416819 |
| ENSE00001553637 | 130414069 | 130414131 |
| ENSE00001553744 | 130418869 | 130418931 |
| ENSE00001553925 | 130423838 | 130423900 |
| ENSE00001554307 | 130373611 | 130373705 |
| ENSE00001555371 | 130406131 | 130406175 |
| ENSE00001556081 | 130405588 | 130405659 |
| ENSE00001557802 | 130391179 | 130391754 |
| ENSE00001559014 | 130426367 | 130426403 |
| ENSE00001559270 | 130397583 | 130397923 |
| ENSE00001559767 | 130403609 | 130403662 |
| ENSE00001560348 | 130379418 | 130380050 |
| ENSE00001560961 | 130422720 | 130422782 |
| ENSE00001561139 | 130413545 | 130413580 |
| ENSE00001561816 | 130410471 | 130410524 |
| ENSE00001562090 | 130406268 | 130406321 |
| ENSE00001562324 | 130376237 | 130376836 |
| ENSE00001562534 | 130394890 | 130395465 |
| ENSE00001562755 | 130401762 | 130401854 |
| ENSE00001563783 | 130426214 | 130426249 |
| ENSE00001564067 | 130388580 | 130389134 |
| ENSE00001564082 | 130421153 | 130421203 |
| ENSE00001564320 | 130384804 | 130385364 |
| ENSE00001634300 | 130471682 | 130471926 |
| ENSE00002055710 | 130484035 | 130484846 |
| ENSE00002421519 | 130429573 | 130429584 |
| ENSE00003970013 | 130345672 | 130345981 |
Expression profiles
Bgee: expression breadth broad, 58 present calls, max score 86.11.
FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0560 / max 11.2069, expressed in 33 samples.
FANTOM5 promoters (1 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 38580 | 0.0560 | 33 |
Top tissues by expression
227 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| upper leg skin | UBERON:0004262 | 86.11 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 76.93 | gold quality |
| upper lobe of left lung | UBERON:0008952 | 74.24 | gold quality |
| upper lobe of lung | UBERON:0008948 | 73.38 | gold quality |
| skin of hip | UBERON:0001554 | 70.21 | gold quality |
| lung | UBERON:0002048 | 69.83 | gold quality |
| right lung | UBERON:0002167 | 68.26 | gold quality |
| lower lobe of lung | UBERON:0008949 | 67.51 | silver quality |
| duodenum | UBERON:0002114 | 61.61 | gold quality |
| skin of abdomen | UBERON:0001416 | 60.14 | gold quality |
| lower esophagus mucosa | UBERON:0035834 | 59.35 | gold quality |
| visceral pleura | UBERON:0002401 | 58.72 | gold quality |
| colonic epithelium | UBERON:0000397 | 55.64 | gold quality |
| zone of skin | UBERON:0000014 | 55.39 | gold quality |
| jejunal mucosa | UBERON:0000399 | 55.09 | gold quality |
| cardia of stomach | UBERON:0001162 | 53.77 | gold quality |
| esophagus mucosa | UBERON:0002469 | 53.39 | gold quality |
| left testis | UBERON:0004533 | 52.64 | gold quality |
| testis | UBERON:0000473 | 51.83 | gold quality |
| urinary bladder | UBERON:0001255 | 51.67 | gold quality |
| bone marrow cell | CL:0002092 | 50.49 | gold quality |
| skin of leg | UBERON:0001511 | 50.40 | gold quality |
| right testis | UBERON:0004534 | 49.53 | gold quality |
| vermiform appendix | UBERON:0001154 | 49.44 | gold quality |
| fundus of stomach | UBERON:0001160 | 49.36 | gold quality |
| caecum | UBERON:0001153 | 48.57 | gold quality |
| jejunum | UBERON:0002115 | 48.29 | gold quality |
| stomach | UBERON:0000945 | 47.35 | gold quality |
| rectum | UBERON:0001052 | 47.35 | gold quality |
| bone marrow | UBERON:0002371 | 46.01 | silver quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 6.66 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
50 targeting COL6A5, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-4692 | 100.00 | 67.32 | 2066 |
| HSA-LET-7A-3P | 100.00 | 74.03 | 3932 |
| HSA-LET-7B-3P | 100.00 | 74.08 | 3913 |
| HSA-LET-7F-1-3P | 100.00 | 74.02 | 3928 |
| HSA-MIR-98-3P | 100.00 | 74.08 | 3907 |
| HSA-MIR-4282 | 99.99 | 75.36 | 6408 |
| HSA-MIR-4514 | 99.99 | 67.10 | 1870 |
| HSA-MIR-4789-5P | 99.98 | 70.76 | 2721 |
| HSA-LET-7F-2-3P | 99.98 | 70.98 | 2588 |
| HSA-MIR-1185-1-3P | 99.98 | 71.04 | 2593 |
| HSA-MIR-1185-2-3P | 99.98 | 71.04 | 2593 |
| HSA-MIR-6793-5P | 99.97 | 65.95 | 758 |
| HSA-MIR-3658 | 99.96 | 73.87 | 4379 |
| HSA-MIR-545-3P | 99.95 | 70.74 | 2783 |
| HSA-MIR-145-5P | 99.92 | 71.13 | 1836 |
| HSA-MIR-5195-3P | 99.92 | 70.92 | 1877 |
| HSA-MIR-4697-3P | 99.89 | 67.09 | 1123 |
| HSA-MIR-221-3P | 99.86 | 71.56 | 1329 |
| HSA-MIR-222-3P | 99.86 | 71.35 | 1337 |
| HSA-MIR-4516 | 99.61 | 67.78 | 3390 |
| HSA-MIR-3120-3P | 99.54 | 70.28 | 2669 |
| HSA-MIR-143-3P | 99.49 | 69.05 | 1457 |
| HSA-MIR-4770 | 99.49 | 69.09 | 1451 |
| HSA-MIR-330-3P | 99.41 | 69.95 | 2521 |
| HSA-MIR-5683 | 99.36 | 68.59 | 2083 |
| HSA-MIR-6088 | 99.29 | 68.45 | 1284 |
| HSA-MIR-4279 | 99.19 | 66.70 | 2437 |
| HSA-MIR-4434 | 99.10 | 67.01 | 1984 |
| HSA-MIR-5703 | 99.10 | 67.09 | 2053 |
| HSA-MIR-7151-3P | 99.04 | 69.72 | 2370 |
Functional genomics
ClinGen dosage: haploinsufficiency 40 (dosage sensitivity unlikely), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map
Literature-anchored findings (GeneRIF, showing 13)
- To identify the underlying atopic dermatitis disease gene, a dense map of microsatellite markers and single nucleotide polymorphisms was used, and association with AD was detected. (PMID:17850181)
- The discovery of three additional collagen VI chains doubles the collagen VI family and adds a layer of complexity to collagen VI assembly and function in the extracellular matrix. (PMID:18400749)
- unlike eczema, genetic variation at COL29A1 and IL31 loci is unlikely to impact inflammatory bowel disease risk (PMID:18839421)
- The role of the COL29A1 gene as an atopic dermatitis gene was not supported. Also, COL29A1 did not play a substantial role in the pathogenesis of chronic obstructive pulmonary disease or asthma. (PMID:20649719)
- localization of alpha5, and to a lesser extent alpha6, is restricted to the papillary dermis, where the protein mainly colocalizes with collagen fibrils; both chains were found around blood vessels (PMID:20882040)
- Our results suggest that COL29A1 is unlikely to contain genetic variants that have a major effect on eczema or atopy susceptibility. (PMID:21353297)
- The collagen VI alpha5 chain is selectively localized at the basement membrane of myotendinous junctions. (PMID:22226732)
- This study demonstrated that an association between COL6A5 gene and familiar chronic itch, suggesting a new contributor to the pathogenesis of neuropathic itch. (PMID:28073787)
- The longitudinal EWAS for the recessive model showed that a novel SNV, rs11917356 of COL6A5, was significantly associated with systolic blood pressure, and the derived allele at the SNV may have spread throughout East Asia in recent evolutionary time. (PMID:29217820)
- three polymorphisms located in COL6A5, COL8A1, and COL10A1 were investigated as potential susceptibility biomarkers for atopic eczema. (PMID:31275967)
- Collagen type VI alpha5 gene variations may predict the risk of lung cancer development in Chinese Han population. (PMID:32193401)
- RNAseq-Based Prioritization Revealed COL6A5, COL8A1, COL10A1 and MIR146A as Common and Differential Susceptibility Biomarkers for Psoriasis and Psoriatic Arthritis: Confirmation from Genotyping Analysis of 1417 Italian Subjects. (PMID:32326527)
- Rare functional genetic variants in COL7A1, COL6A5, COL1A2 and COL5A2 frequently occur in Chiari Malformation Type 1. (PMID:33974636)
Cross-species orthologs
4 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| mus_musculus | Col6a5 | ENSMUSG00000091345 |
| rattus_norvegicus | Col6a5 | ENSRNOG00000010663 |
| caenorhabditis_elegans | WBGENE00003497 | |
| caenorhabditis_elegans | WBGENE00007800 |
Paralogs (12): COCH (ENSG00000100473), COL12A1 (ENSG00000111799), MATN4 (ENSG00000124159), MATN3 (ENSG00000132031), MATN2 (ENSG00000132561), MATN1 (ENSG00000162510), COL6A3 (ENSG00000163359), VWA2 (ENSG00000165816), VWA1 (ENSG00000179403), COL14A1 (ENSG00000187955), VIT (ENSG00000205221), COL6A6 (ENSG00000206384)
Protein
Protein identifiers
Collagen alpha-5(VI) chain — A8TX70 (reviewed: A8TX70)
Alternative names: Collagen alpha-1(XXIX) chain, von Willebrand factor A domain-containing protein 4
All UniProt accessions (4): A8TX70, H0Y393, H0Y935, H0Y9T2
UniProt curated annotations — full annotation on UniProt →
Function. Collagen VI acts as a cell-binding protein.
Subunit / interactions. Trimers composed of three different chains: alpha-1(VI), alpha-2(VI), and alpha-3(VI) or alpha-5(VI) or alpha-6(VI).
Subcellular location. Secreted. Extracellular space. Extracellular matrix.
Tissue specificity. Expressed in skin, followed by lung, small intestine, colon and testis. In skin, it is expressed in the epidermis with strongest staining in suprabasal viable layers. In ATOD patients, it is absent in the most differentiated upper spinous and granular layers (at protein level).
Post-translational modifications. Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains.
Disease relevance. Patients affected by atopic dermatitis display an abnormal distribution of COL29A1 mRNA and protein in skin suggesting that COL29A1 may be involved in the pathogenesis of the disease.
Similarity. Belongs to the type VI collagen family.
Isoforms (2)
| UniProt ID | Names | Canonical? |
|---|---|---|
| A8TX70-1 | 1 | yes |
| A8TX70-2 | 2 |
RefSeq proteins (3): NP_001265227, NP_001399086, NP_694996 (=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR002035 | VWF_A | Domain |
| IPR008160 | Collagen | Repeat |
| IPR036465 | vWFA_dom_sf | Homologous_superfamily |
| IPR050525 | ECM_Assembly_Org | Family |
Pfam: PF00092, PF01391
UniProt features (46 total): domain 16, sequence variant 11, region of interest 4, glycosylation site 4, compositionally biased region 3, sequence conflict 3, splice variant 2, signal peptide 1, chain 1, short sequence motif 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-A8TX70-F1 | 70.94 | 0.17 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Glycosylation sites (4): 201, 260, 835, 2509
Function
Pathways and Gene Ontology
Reactome pathways
8 pathways
| ID | Pathway |
|---|---|
| R-HSA-1442490 | Collagen degradation |
| R-HSA-1650814 | Collagen biosynthesis and modifying enzymes |
| R-HSA-186797 | Signaling by PDGF |
| R-HSA-2022090 | Assembly of collagen fibrils and other multimeric structures |
| R-HSA-216083 | Integrin cell surface interactions |
| R-HSA-3000178 | ECM proteoglycans |
| R-HSA-419037 | NCAM1 interactions |
| R-HSA-8948216 | Collagen chain trimerization |
MSigDB gene sets: 66 (showing top):
GOCC_COLLAGEN_TRIMER, REACTOME_NCAM_SIGNALING_FOR_NEURITE_OUT_GROWTH, GOMF_EXTRACELLULAR_MATRIX_STRUCTURAL_CONSTITUENT, chr3q22, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, REACTOME_INTEGRIN_CELL_SURFACE_INTERACTIONS, GOCC_COMPLEX_OF_COLLAGEN_TRIMERS, GOMF_STRUCTURAL_MOLECULE_ACTIVITY, REACTOME_SIGNALING_BY_PDGF, GOCC_SUPRAMOLECULAR_COMPLEX, GOMF_EXTRACELLULAR_MATRIX_STRUCTURAL_CONSTITUENT_CONFERRING_TENSILE_STRENGTH, REACTOME_COLLAGEN_DEGRADATION, REACTOME_COLLAGEN_BIOSYNTHESIS_AND_MODIFYING_ENZYMES, REACTOME_ASSEMBLY_OF_COLLAGEN_FIBRILS_AND_OTHER_MULTIMERIC_STRUCTURES, REACTOME_ECM_PROTEOGLYCANS
GO Biological Process (2): cell adhesion (GO:0007155), extracellular matrix organization (GO:0030198)
GO Molecular Function (2): extracellular matrix structural constituent conferring tensile strength (GO:0030020), protein binding (GO:0005515)
GO Cellular Component (4): extracellular region (GO:0005576), collagen type VI trimer (GO:0005589), extracellular matrix (GO:0031012), collagen trimer (GO:0005581)
Reactome top-level categories
Rollup of top-6 pathways:
| Category | Pathways |
|---|---|
| Collagen formation | 2 |
| Extracellular matrix organization | 2 |
| Degradation of the extracellular matrix | 1 |
| Signaling by Receptor Tyrosine Kinases | 1 |
| NCAM signaling for neurite out-growth | 1 |
| Collagen biosynthesis and modifying enzymes | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular process | 1 |
| extracellular structure organization | 1 |
| external encapsulating structure organization | 1 |
| extracellular matrix structural constituent | 1 |
| binding | 1 |
| cellular anatomical structure | 1 |
| collagen beaded filament | 1 |
| von-Willerbrand-factor-A-domain-rich collagen trimer | 1 |
| extracellular protein-containing complex | 1 |
| external encapsulating structure | 1 |
| protein-containing complex | 1 |
Protein interactions and networks
STRING
1080 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| COL6A5 | CSTA | P01040 | 884 |
| COL6A5 | MS4A2 | Q01362 | 767 |
| COL6A5 | CMA1 | P23946 | 650 |
| COL6A5 | COL6A2 | P12110 | 564 |
| COL6A5 | COL5A2 | P05997 | 485 |
| COL6A5 | COL5A1 | P20908 | 484 |
| COL6A5 | COL6A1 | P12109 | 482 |
| COL6A5 | ARMH1 | Q6PIY5 | 470 |
| COL6A5 | ACAD10 | Q6JQN1 | 469 |
| COL6A5 | COL1A2 | P02464 | 466 |
| COL6A5 | ADAMTS2 | O95450 | 440 |
| COL6A5 | COL8A1 | P27658 | 436 |
| COL6A5 | COL2A1 | P02458 | 416 |
| COL6A5 | F2RL2 | O00254 | 402 |
| COL6A5 | CLCA2 | Q9UQC9 | 396 |
IntAct
0 interactions, top by confidence:
BioGRID (6): COL6A5 (Affinity Capture-MS), COL6A5 (Affinity Capture-MS), COL6A5 (Reconstituted Complex), COL6A5 (Affinity Capture-Western), USP3 (Affinity Capture-Western), YWHAE (Cross-Linking-MS (XL-MS))
ESM2 similar proteins: A2AX52, A6H584, A6NMZ7, A6X935, A8TX70, E1BMV3, E7FF10, O00339, O02668, O08746, O55123, O89029, P05099, P06681, P12111, P15989, P19823, P19827, P21180, P21941, P51942, P79263, P97278, P97279, Q0IIH7, Q0V8T0, Q0V8T5, Q0V8T6, Q0V8T7, Q0VCM5, Q14624, Q21540, Q29052, Q3SYW2, Q3T052, Q5GFL6, Q61702, Q61703, Q6DCQ6, Q70UZ7
Diamond homologs: A2AX52, A6H584, A6NMZ7, A6QLN9, A8TX70, E7FF10, O00339, O08746, O42401, O75578, O89029, P05099, P05555, P11215, P12111, P15989, P20701, P20702, P34576, P51942, P61625, Q02388, Q13349, Q21281, Q21540, Q28902, Q3V0T4, Q63870, Q642A6, Q6PCB0, Q6UXI7, Q8C6K9, Q8NFW1, Q8R2Z5, Q90615, Q91145, Q923P0, Q95LI2, Q96P44, Q9P218
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
406 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 321 |
| Likely benign | 55 |
| Benign | 12 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
6467 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 3:130345977:GCTGG:G | donor_gain | 1.0000 |
| 3:130345979:TGGG:T | donor_loss | 1.0000 |
| 3:130345980:GG:G | donor_gain | 1.0000 |
| 3:130345981:GG:G | donor_gain | 1.0000 |
| 3:130345982:GTAA:G | donor_loss | 1.0000 |
| 3:130345983:T:A | donor_loss | 1.0000 |
| 3:130376223:T:G | acceptor_gain | 1.0000 |
| 3:130376227:A:AG | acceptor_gain | 1.0000 |
| 3:130376227:ATTTT:A | acceptor_gain | 1.0000 |
| 3:130376228:T:G | acceptor_gain | 1.0000 |
| 3:130376231:T:A | acceptor_gain | 1.0000 |
| 3:130376235:A:AG | acceptor_gain | 1.0000 |
| 3:130376235:AG:A | acceptor_gain | 1.0000 |
| 3:130376235:AGG:A | acceptor_gain | 1.0000 |
| 3:130376236:G:GA | acceptor_gain | 1.0000 |
| 3:130376236:GG:G | acceptor_gain | 1.0000 |
| 3:130376236:GGG:G | acceptor_gain | 1.0000 |
| 3:130376236:GGGC:G | acceptor_gain | 1.0000 |
| 3:130376236:GGGCC:G | acceptor_gain | 1.0000 |
| 3:130391613:G:GG | donor_gain | 1.0000 |
| 3:130394886:GCA:G | acceptor_loss | 1.0000 |
| 3:130394887:CA:C | acceptor_loss | 1.0000 |
| 3:130394888:A:AG | acceptor_gain | 1.0000 |
| 3:130394888:AGTCT:A | acceptor_gain | 1.0000 |
| 3:130394889:G:GA | acceptor_gain | 1.0000 |
| 3:130394889:GT:G | acceptor_gain | 1.0000 |
| 3:130394889:GTC:G | acceptor_gain | 1.0000 |
| 3:130394889:GTCT:G | acceptor_gain | 1.0000 |
| 3:130394889:GTCTG:G | acceptor_gain | 1.0000 |
| 3:130395462:ACCA:A | donor_gain | 1.0000 |
AlphaMissense
17346 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 3:130376267:T:C | F33S | 0.986 |
| 3:130376413:T:C | F82L | 0.986 |
| 3:130376415:C:A | F82L | 0.986 |
| 3:130376415:C:G | F82L | 0.986 |
| 3:130388732:T:C | F672L | 0.985 |
| 3:130388734:C:A | F672L | 0.985 |
| 3:130388734:C:G | F672L | 0.985 |
| 3:130376270:T:C | L34P | 0.984 |
| 3:130469013:G:C | A2337P | 0.984 |
| 3:130376278:A:C | S37R | 0.983 |
| 3:130376280:C:A | S37R | 0.983 |
| 3:130376280:C:G | S37R | 0.983 |
| 3:130376377:G:C | A70P | 0.983 |
| 3:130376588:T:A | V140D | 0.983 |
| 3:130376510:T:C | L114P | 0.982 |
| 3:130379577:T:C | L276P | 0.981 |
| 3:130440225:G:C | D1963H | 0.981 |
| 3:130440723:A:C | S2129R | 0.981 |
| 3:130440725:C:A | S2129R | 0.981 |
| 3:130440725:C:G | S2129R | 0.981 |
| 3:130376381:T:C | L71P | 0.980 |
| 3:130388913:T:C | L732P | 0.980 |
| 3:130376275:G:C | D36H | 0.978 |
| 3:130376383:G:C | A72P | 0.978 |
| 3:130440654:T:A | C2106S | 0.978 |
| 3:130440655:G:C | C2106S | 0.978 |
| 3:130379466:T:C | F239S | 0.977 |
| 3:130388621:A:C | S635R | 0.977 |
| 3:130388623:T:A | S635R | 0.977 |
| 3:130388623:T:G | S635R | 0.977 |
dbSNP variants (sampled 300 via entrez): RS1000011069 (3:130477402 C>G,T), RS1000030150 (3:130459395 G>A), RS1000055271 (3:130392593 T>G), RS1000058199 (3:130452890 A>G), RS1000060714 (3:130381657 C>T), RS1000077444 (3:130388285 C>T), RS1000099240 (3:130344243 A>G), RS1000110166 (3:130472241 C>T), RS1000138548 (3:130430107 G>A), RS1000159622 (3:130374910 AG>A), RS1000160525 (3:130418137 T>C), RS1000232022 (3:130478778 G>C,T), RS1000256703 (3:130394314 T>C), RS1000292961 (3:130423452 G>C), RS1000358008 (3:130361110 C>A)
Disease associations
OMIM: gene MIM:611916 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
7 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST002301_3 | Body mass index | 1.000000e-08 |
| GCST004748_85 | Lung cancer | 8.000000e-06 |
| GCST008158_145 | Body mass index | 7.000000e-06 |
| GCST010477_4 | Hypertension | 4.000000e-07 |
| GCST010478_1 | Chronic kidney disease | 5.000000e-09 |
| GCST012490_588 | Femur bone mineral density x serum urate levels interaction | 8.000000e-11 |
| GCST90020028_1720 | Hip circumference adjusted for BMI | 3.000000e-08 |
EFO canonical traits (3, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0004340 | body mass index |
| EFO:0004531 | urate measurement |
| EFO:0008039 | BMI-adjusted hip circumference |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: yes
ChEMBL targets (1): CHEMBL2364188 (PROTEIN COMPLEX GROUP)
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
12 total (human), top 12 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Nickel | increases expression | 2 |
| bisphenol A | increases methylation | 1 |
| sodium arsenite | increases expression | 1 |
| S-(1,2-dichlorovinyl)cysteine | affects response to substance, increases expression | 1 |
| bisphenol S | affects cotreatment, increases methylation | 1 |
| MT19c compound | decreases expression | 1 |
| Fulvestrant | affects cotreatment, increases methylation | 1 |
| Acetaminophen | decreases expression | 1 |
| Benzo(a)pyrene | affects methylation | 1 |
| Lipopolysaccharides | affects response to substance, increases expression | 1 |
| Triclosan | increases expression | 1 |
| Aflatoxin B1 | increases methylation | 1 |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.