COL16A1

Summary

COL16A1 (collagen type XVI alpha 1 chain, HGNC:2193) is a protein-coding gene on chromosome 1p35.2, encoding Collagen alpha-1(XVI) chain (Q07092). Involved in mediating cell attachment and inducing integrin-mediated cellular reactions, such as cell spreading and alterations in cell morphology.

This gene encodes the alpha chain of type XVI collagen, a member of the FACIT collagen family (fibril-associated collagens with interrupted helices). Members of this collagen family are found in association with fibril-forming collagens such as type I and II, and serve to maintain the integrity of the extracellular matrix. High levels of type XVI collagen have been found in fibroblasts and keratinocytes, and in smooth muscle and amnion.

Source: NCBI Gene 1307 — RefSeq curated summary.

At a glance

• GWAS associations: 13
• Clinical variants (ClinVar): 336 total
• Dosage sensitivity (ClinGen): haploinsufficiency dosage sensitivity unlikely, triplosensitivity no evidence
• MANE Select transcript: NM_001856

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:2193
Approved symbol	COL16A1
Name	collagen type XVI alpha 1 chain
Location	1p35.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000084636
Ensembl biotype	protein_coding
OMIM	120326
Entrez	1307

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 8 protein_coding, 7 protein_coding_CDS_not_defined, 5 retained_intron

ENST00000373667, ENST00000373668, ENST00000373672, ENST00000440437, ENST00000458715, ENST00000461217, ENST00000466829, ENST00000468459, ENST00000470799, ENST00000474000, ENST00000479100, ENST00000482478, ENST00000482910, ENST00000488128, ENST00000488897, ENST00000529928, ENST00000532877, ENST00000873809, ENST00000873810, ENST00000933935

RefSeq mRNA: 1 — MANE Select: NM_001856 NM_001856

CCDS: CCDS41297

Canonical transcript exons

ENST00000373672 — 71 exons

Exon	Start	End
ENSE00000957114	31697220	31697300
ENSE00000957124	31679632	31679685
ENSE00001049296	31683334	31683369
ENSE00001049300	31696088	31696141
ENSE00001049305	31692767	31692808
ENSE00001049313	31692598	31692642
ENSE00001049317	31689741	31689851
ENSE00001049318	31692005	31692067
ENSE00001049321	31682934	31683002
ENSE00001049334	31692474	31692509
ENSE00001049341	31683707	31683748
ENSE00001049351	31675258	31675311
ENSE00001049353	31683194	31683247
ENSE00001049354	31684109	31684231
ENSE00001049356	31696963	31697088
ENSE00001302737	31693092	31693154
ENSE00001317341	31691598	31691642
ENSE00001351488	31679804	31679851
ENSE00001367413	31691188	31691226
ENSE00001370390	31690367	31690393
ENSE00001374034	31690529	31690573
ENSE00001389259	31691417	31691512
ENSE00001408743	31680905	31680931
ENSE00001411271	31680042	31680101
ENSE00001416670	31695761	31695787
ENSE00001425258	31670602	31670646
ENSE00001426345	31652263	31652853
ENSE00001431648	31681023	31681067
ENSE00001461224	31675007	31675039
ENSE00001461262	31694144	31694170
ENSE00001461263	31695186	31695221
ENSE00001684687	31698483	31698606
ENSE00001769021	31702121	31702227
ENSE00001786800	31697906	31698172
ENSE00003459843	31700041	31700115
ENSE00003465425	31665882	31665935
ENSE00003469187	31685639	31685770
ENSE00003470110	31665583	31665618
ENSE00003471178	31666037	31666081
ENSE00003473792	31653867	31654043
ENSE00003475432	31671615	31671659
ENSE00003487094	31672596	31672637
ENSE00003489302	31686244	31686279
ENSE00003490591	31655314	31655502
ENSE00003504720	31667575	31667628
ENSE00003506580	31689050	31689085
ENSE00003508173	31662334	31662387
ENSE00003509342	31665172	31665234
ENSE00003512132	31662587	31662658
ENSE00003518166	31661660	31661704
ENSE00003529403	31657033	31657068
ENSE00003530739	31660585	31660638
ENSE00003538372	31683950	31684003
ENSE00003541815	31684821	31684856
ENSE00003544539	31668802	31668855
ENSE00003567665	31661414	31661458
ENSE00003569556	31668165	31668218
ENSE00003572798	31654792	31654858
ENSE00003585330	31658914	31658964
ENSE00003609461	31688467	31688502
ENSE00003624509	31699813	31699930
ENSE00003645329	31653599	31653676
ENSE00003651886	31684523	31684630
ENSE00003653597	31658488	31658577
ENSE00003658602	31686091	31686135
ENSE00003663260	31661066	31661119
ENSE00003672238	31672416	31672502
ENSE00003692795	31672724	31672840
ENSE00003786822	31688861	31688971
ENSE00003787901	31656400	31656444
ENSE00003841527	31703837	31704017

Expression profiles

Bgee: expression breadth ubiquitous, 282 present calls, max score 99.15.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.0891 / max 432.3877, expressed in 992 samples.

FANTOM5 promoters (12 alternative TSS)

Promoter ID	TPM avg	Samples expressed
11480	8.8743	794
11479	7.5567	764
11484	1.2806	438
11482	0.9138	405
11483	0.3957	215
11481	0.3933	210
11472	0.3851	183
11486	0.1161	56
11474	0.0487	20
11485	0.0470	26

Top tissues by expression

290 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
tibia	UBERON:0000979	99.15	gold quality
cartilage tissue	UBERON:0002418	98.97	gold quality
left ovary	UBERON:0002119	98.72	gold quality
endocervix	UBERON:0000458	98.71	gold quality
sural nerve	UBERON:0015488	98.66	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	98.54	gold quality
right ovary	UBERON:0002118	98.40	gold quality
right coronary artery	UBERON:0001625	98.05	gold quality
spinal cord	UBERON:0002240	98.02	gold quality
body of uterus	UBERON:0009853	98.02	gold quality
periodontal ligament	UBERON:0008266	97.91	gold quality
mucosa of stomach	UBERON:0001199	97.82	gold quality
ascending aorta	UBERON:0001496	97.81	gold quality
thoracic aorta	UBERON:0001515	97.78	gold quality
ectocervix	UBERON:0012249	97.71	gold quality
descending thoracic aorta	UBERON:0002345	97.69	gold quality
middle frontal gyrus	UBERON:0002702	97.66	gold quality
tibial nerve	UBERON:0001323	97.60	gold quality
tendon of biceps brachii	UBERON:0008188	97.47	gold quality
right lobe of thyroid gland	UBERON:0001119	97.34	gold quality
colonic epithelium	UBERON:0000397	97.19	gold quality
muscle layer of sigmoid colon	UBERON:0035805	97.17	gold quality
aorta	UBERON:0000947	97.16	gold quality
left lobe of thyroid gland	UBERON:0001120	97.04	gold quality
right testis	UBERON:0004534	97.04	gold quality
skin of abdomen	UBERON:0001416	97.01	gold quality
skin of leg	UBERON:0001511	96.94	gold quality
left testis	UBERON:0004533	96.91	gold quality
saphenous vein	UBERON:0007318	96.89	gold quality
popliteal artery	UBERON:0002250	96.75	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	17.92
E-CURD-119	yes	9.63
E-GEOD-124858	no	58.25

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

37 targeting COL16A1, 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-4795-3P	100.00	74.62	4024
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-6797-5P	99.61	66.55	2084
HSA-MIR-5003-5P	99.61	69.13	1624
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-543	99.52	69.03	2595
HSA-MIR-6832-3P	99.52	70.44	1726
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-6830-3P	98.62	68.07	1760
HSA-MIR-4436B-3P	98.25	65.26	1494
HSA-MIR-5585-3P	98.25	67.41	941
HSA-MIR-6735-5P	98.24	65.36	1488
HSA-MIR-7843-5P	98.12	65.26	1421
HSA-MIR-6742-3P	97.95	64.50	1490
HSA-MIR-3159	97.94	66.79	1098

Functional genomics

ClinGen dosage: haploinsufficiency 40 (dosage sensitivity unlikely), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 9)

• Not in banded collagen fibrils in dermis, but is component of specialized fibrillin-1-containing microfibrils. In cartilage matrix not in aggregates with fibrillin-1. Resides in thin, weakly banded collagen fibrils also containing collagens II and XI. (PMID:12782140)
• interacts with fibrillin-1 and with fibronectin indicating multiple molecular interactions in which this ubiquitously expressed and versatile fibril-associated collagens with interrupted triple helices-collagen can participate (PMID:15165854)
• These results demonstrate de-novo expression of collagen XVI in glioblastomas as part of the tumor specific remodeling of the ECM. (PMID:18804107)
• Collagen XVI promotes persistence of intestinal subepithelial myofibroblasts in the normal and in the inflamed bowel wall by stabilizing focal adhesion contacts. (PMID:19931388)
• Overexpression of type XVI collagen in aberrant oral keratinocytes leads to Kindlin-1 induction, increased Kindlin-1/beta1-integrin interaction, integrin activation and subsequently to a proliferative cellular phenotype. (PMID:21251976)
• Gene expression profiles showed that COL16A1 was up-regulated in epidermolysis bullosa subtypes. (PMID:22716248)
• collagen XVI plays a decisive role in the interaction of connective tissue cells with their ECM, which is impaired in pathological situations (PMID:23149016)
• High Collagen XVI expression is associated with invasion of oral squamous cell carcinoma. (PMID:24466237)
• The NC11 domain of collagen XVI is a potential biomarker for oral squamous cell carcinoma and triggers vasculogenic mimicry via upregulation of endothelial receptors VEGFR1, VEGFR2 and uPAR. (PMID:26424749)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Col16a1	ENSMUSG00000040690
rattus_norvegicus	Col16a1	ENSRNOG00000031475

Paralogs (37): COL9A2 (ENSG00000049089), COL23A1 (ENSG00000050767), COL11A1 (ENSG00000060718), COL17A1 (ENSG00000065618), COL5A3 (ENSG00000080573), COL4A4 (ENSG00000081052), COL9A3 (ENSG00000092758), COL20A1 (ENSG00000101203), COL1A1 (ENSG00000108821), COL9A1 (ENSG00000112280), COL7A1 (ENSG00000114270), COL21A1 (ENSG00000124749), COL5A1 (ENSG00000130635), COL4A2 (ENSG00000134871), COL2A1 (ENSG00000139219), COL6A1 (ENSG00000142156), COL6A2 (ENSG00000142173), EDA (ENSG00000158813), COL26A1 (ENSG00000160963), COL1A2 (ENSG00000164692), COL3A1 (ENSG00000168542), COL4A3 (ENSG00000169031), COL22A1 (ENSG00000169436), COL24A1 (ENSG00000171502), COL18A1 (ENSG00000182871), EMID1 (ENSG00000186998), COL4A1 (ENSG00000187498), COL4A5 (ENSG00000188153), COL25A1 (ENSG00000188517), COL27A1 (ENSG00000196739), COL13A1 (ENSG00000197467), COL4A6 (ENSG00000197565), COL11A2 (ENSG00000204248), COL5A2 (ENSG00000204262), COL15A1 (ENSG00000204291), COLQ (ENSG00000206561), COL28A1 (ENSG00000215018)

Protein

Protein identifiers

Collagen alpha-1(XVI) chain — Q07092 (reviewed: Q07092)

All UniProt accessions (5): Q07092, A6NCT7, H7BY97, H7BZL8, H7C3F0

UniProt curated annotations — full annotation on UniProt →

Function. Involved in mediating cell attachment and inducing integrin-mediated cellular reactions, such as cell spreading and alterations in cell morphology.

Subunit / interactions. Homotrimer. Interacts with FBN1, fibronectin and integrins ITGA1/ITGB1 and ITGA2/ITGB1. Integrin ITGA1/ITGB1 binds to a unique site within COL16A1 located close to its C-terminal end between collagenous domains COL1-COL3.

Subcellular location. Secreted. Extracellular space. Extracellular matrix.

Tissue specificity. In papillary dermis, is a component of specialized fibrillin-1-containing microfibrils, whereas in territorial cartilage matrix, it is localized to a discrete population of thin, weakly banded collagen fibrils in association with other collagens (at protein level). In the placenta, where it is found in the amnion, a membranous tissue lining the amniotic cavity. Within the amnion, it is found in an acellular, relatively dense layer of a complex network of reticular fibers. Also located to a fibroblast layer beneath this dense layer. Exists in tissues in association with other types of collagen.

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. Glycosylated.

Domain organisation. This sequence defines eighteen different domains, nine triple-helical domains (COL9 to COL1) and ten non-triple-helical domains (NC10 to NC1). The numerous interruptions in the triple helix may make this molecule either elastic or flexible.

Similarity. Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q07092-1	1	yes
Q07092-2	2

RefSeq proteins (1): NP_001847* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008160	Collagen	Repeat
IPR013320	ConA-like_dom_sf	Homologous_superfamily
IPR048287	TSPN-like_N	Domain
IPR050149	Collagen_superfamily	Family

Pfam: PF01391

UniProt features (73 total): region of interest 23, compositionally biased region 22, domain 9, sequence conflict 7, short sequence motif 3, sequence variant 3, glycosylation site 2, splice variant 2, signal peptide 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q07092-F1	49.60	0.11

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 (2): 47, 327

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-1442490	Collagen degradation
R-HSA-1650814	Collagen biosynthesis and modifying enzymes
R-HSA-216083	Integrin cell surface interactions
R-HSA-8948216	Collagen chain trimerization

MSigDB gene sets: 228 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, CREL_01, JI_RESPONSE_TO_FSH_UP, MACLACHLAN_BRCA1_TARGETS_DN, GOBP_RESPONSE_TO_ACID_CHEMICAL, GOCC_COLLAGEN_TRIMER, GCM_NPM1, GOBP_FOCAL_ADHESION_ASSEMBLY, ASTON_MAJOR_DEPRESSIVE_DISORDER_DN, MCBRYAN_PUBERTAL_TGFB1_TARGETS_UP, GOBP_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, GOBP_CELLULAR_RESPONSE_TO_ACID_CHEMICAL, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, LIEN_BREAST_CARCINOMA_METAPLASTIC, HUMMERICH_SKIN_CANCER_PROGRESSION_DN

GO Biological Process (7): cell adhesion (GO:0007155), integrin-mediated signaling pathway (GO:0007229), female pregnancy (GO:0007565), integrin activation (GO:0033622), cell adhesion mediated by integrin (GO:0033627), positive regulation of focal adhesion assembly (GO:0051894), cellular response to amino acid stimulus (GO:0071230)

GO Molecular Function (3): integrin binding (GO:0005178), extracellular matrix structural constituent conferring tensile strength (GO:0030020), protein binding (GO:0005515)

GO Cellular Component (6): extracellular region (GO:0005576), collagen type XVI trimer (GO:0005597), basement membrane (GO:0005604), endoplasmic reticulum lumen (GO:0005788), extracellular matrix (GO:0031012), collagen trimer (GO:0005581)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
Degradation of the extracellular matrix	1
Collagen formation	1
Extracellular matrix organization	1
Collagen biosynthesis and modifying enzymes	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular process	1
cell surface receptor signaling pathway	1
multi-organism reproductive process	1
multi-multicellular organism process	1
protein-containing complex assembly	1
cell adhesion	1
positive regulation of cell-matrix adhesion	1
focal adhesion assembly	1
regulation of focal adhesion assembly	1
positive regulation of cell-substrate junction organization	1
positive regulation of cell junction assembly	1
response to amino acid	1
cellular response to acid chemical	1
signaling receptor binding	1
protein-containing complex binding	1
cell adhesion molecule binding	1
extracellular matrix structural constituent	1
binding	1
cellular anatomical structure	1
FACIT collagen trimer	1
extracellular matrix	1
endoplasmic reticulum	1
intracellular organelle lumen	1
external encapsulating structure	1
protein-containing complex	1

Protein interactions and networks

STRING

1632 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
COL16A1	FBN1	P35555	540
COL16A1	COL27A1	Q8IZC6	531
COL16A1	COL6A3	P12111	527
COL16A1	JUN	P05412	521
COL16A1	ADAMTS10	Q9H324	520
COL16A1	ADAMTSL2	Q86TH1	516
COL16A1	COL14A1	Q05707	504
COL16A1	COL4A2	P08572	503
COL16A1	SLC8A2	Q9UPR5	502
COL16A1	COL5A3	P25940	501
COL16A1	COL5A2	P05997	495
COL16A1	COL11A1	P12107	492
COL16A1	COL3A1	P02461	486
COL16A1	SLC6A1	P30531	478
COL16A1	COL1A2	P02464	468

IntAct

12 interactions, top by confidence:

A	B	Type	Score
MMP2	COL4A1	psi-mi:“MI:0914”(association)	0.640
LAIR2	LAMA5	psi-mi:“MI:0914”(association)	0.530
COL16A1	H1-2	psi-mi:“MI:0915”(physical association)	0.400
COL16A1	TCOF1	psi-mi:“MI:0915”(physical association)	0.400
COL16A1	PLOD3	psi-mi:“MI:0914”(association)	0.350
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350
C1QTNF1	CALU	psi-mi:“MI:0914”(association)	0.350
P4HA2	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
COL16A1	GFAP	psi-mi:“MI:0403”(colocalization)	0.270
COL4A1	COL16A1	psi-mi:“MI:0403”(colocalization)	0.270
COL16A1	yhjW	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (17): COL16A1 (Proximity Label-MS), TCOF1 (Proximity Label-MS), COL16A1 (Proximity Label-MS), COL16A1 (Affinity Capture-RNA), COLGALT2 (Affinity Capture-MS), IPP (Affinity Capture-MS), PLOD3 (Affinity Capture-MS), P4HA1 (Affinity Capture-MS), PLOD1 (Affinity Capture-MS), KLHL12 (Affinity Capture-MS), TUBB8 (Affinity Capture-MS), COL16A1 (Affinity Capture-MS), COL16A1 (Proximity Label-MS), HSP90AB1 (Cross-Linking-MS (XL-MS)), COL16A1 (Proximity Label-MS)

ESM2 similar proteins: A0A060WQA3, A0MSJ1, A5PN28, A6NHN0, A8WGB1, A8WR59, B2RNN3, B7Z0K8, C7DZK3, O35167, O35348, O76368, O88207, P0C862, P12107, P13942, P20908, P20909, P23805, P25067, P25318, P25940, P42916, P83371, P98085, Q03637, Q07092, Q07563, Q0II24, Q0VF58, Q17RW2, Q30D77, Q32S24, Q3MI99, Q4ZJM7, Q4ZJN1, Q60467, Q61245, Q64739, Q6UXH8

Diamond homologs: A0MSJ1, B8V7R6, C0HM88, C7DZK3, O42350, O46392, O88207, O93484, P02452, P02453, P02454, P02457, P02458, P02459, P02460, P02461, P02465, P02466, P02467, P05539, P05997, P08121, P08123, P11087, P12105, P12107, P13941, P13942, P18856, P20908, P20909, P25940, P28481, Q01149, Q07092, Q17RW2, Q28083, Q28668, Q30D77, Q32S24

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

336 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	230
Likely benign	15
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

9779 predictions. Top by Δscore:

Variant	Effect	Δscore
1:31653595:CTACC:C	donor_loss	1.0000
1:31653596:TACC:T	donor_loss	1.0000
1:31653597:ACC:A	donor_loss	1.0000
1:31653598:C:CA	donor_loss	1.0000
1:31653672:CAATC:C	acceptor_gain	1.0000
1:31653673:AATC:A	acceptor_gain	1.0000
1:31653674:ATC:A	acceptor_gain	1.0000
1:31653675:TC:T	acceptor_gain	1.0000
1:31653676:CC:C	acceptor_gain	1.0000
1:31653677:C:CA	acceptor_loss	1.0000
1:31653677:C:CC	acceptor_gain	1.0000
1:31653678:T:C	acceptor_loss	1.0000
1:31653813:AGG:A	donor_gain	1.0000
1:31653872:A:AC	donor_gain	1.0000
1:31653872:ACT:A	donor_gain	1.0000
1:31653873:C:CC	donor_gain	1.0000
1:31653873:CT:C	donor_gain	1.0000
1:31653873:CTC:C	donor_gain	1.0000
1:31653892:T:TA	donor_gain	1.0000
1:31653959:T:TA	donor_gain	1.0000
1:31653963:T:TA	donor_gain	1.0000
1:31653964:C:A	donor_gain	1.0000
1:31658486:A:AC	donor_gain	1.0000
1:31658487:C:CC	donor_gain	1.0000
1:31660583:A:AC	donor_gain	1.0000
1:31660584:C:CC	donor_gain	1.0000
1:31660584:CAA:C	donor_gain	1.0000
1:31660649:C:CT	acceptor_gain	1.0000
1:31660650:A:T	acceptor_gain	1.0000
1:31661700:TCCCC:T	acceptor_gain	1.0000

AlphaMissense

10121 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:31696995:A:G	C278R	0.996
1:31691624:A:G	C426R	0.995
1:31696987:G:C	C280W	0.995
1:31696989:A:G	C280R	0.995
1:31696994:C:G	C278S	0.995
1:31696995:A:T	C278S	0.995
1:31661439:C:T	G1249E	0.994
1:31661449:C:G	G1246R	0.994
1:31661449:C:T	G1246R	0.994
1:31696993:G:C	C278W	0.994
1:31661457:C:T	G1243D	0.993
1:31691622:A:C	C426W	0.993
1:31696988:C:G	C280S	0.993
1:31696989:A:T	C280S	0.993
1:31661430:C:T	G1252D	0.992
1:31661448:C:T	G1246E	0.992
1:31661449:C:A	G1246W	0.992
1:31691623:C:G	C426S	0.992
1:31691624:A:T	C426S	0.992
1:31696988:C:T	C280Y	0.992
1:31665599:C:T	G1159D	0.991
1:31661109:C:T	G1261D	0.990
1:31665233:C:T	G1165D	0.990
1:31665590:C:T	G1162D	0.990
1:31667627:C:T	G1102D	0.990
1:31691623:C:T	C426Y	0.990
1:31652733:C:G	C1578S	0.989
1:31652734:A:T	C1578S	0.989
1:31661119:C:G	G1258R	0.989
1:31665197:C:T	G1177D	0.989

dbSNP variants (sampled 300 via entrez): RS1000062415 (1:31672242 A>G), RS1000217320 (1:31666248 G>A), RS1000401131 (1:31695286 A>C,G), RS1000427270 (1:31695000 A>G), RS1000432758 (1:31654953 A>G), RS1000481120 (1:31667700 G>A,C), RS1000733341 (1:31696889 C>A,T), RS1000822731 (1:31656194 A>G), RS1000890257 (1:31654628 T>C), RS1000914298 (1:31679407 A>T), RS1001011006 (1:31685193 T>C), RS1001045832 (1:31660715 GC>G), RS1001068451 (1:31684914 G>A,C), RS1001172952 (1:31656560 C>G,T), RS1001173776 (1:31680793 A>G)

Disease associations

OMIM: gene MIM:120326 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

13 associations (top):

Study	Trait	p-value
GCST002783_316	Body mass index	5.000000e-06
GCST005316_272	Intelligence (MTAG)	7.000000e-10
GCST005316_435	Intelligence (MTAG)	1.000000e-14
GCST005316_436	Intelligence (MTAG)	8.000000e-10
GCST005316_438	Intelligence (MTAG)	2.000000e-13
GCST005316_439	Intelligence (MTAG)	3.000000e-12
GCST005951_36	Body mass index	9.000000e-10
GCST006269_1092	General cognitive ability	5.000000e-11
GCST006269_800	General cognitive ability	7.000000e-09
GCST006957_1	Severe aortic features in Marfan syndrome	9.000000e-06
GCST009798_61	Asthma	3.000000e-08
GCST010042_96	Asthma	3.000000e-08
GCST010043_82	Asthma	2.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0004337	intelligence

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

46 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases methylation, increases expression	3
bisphenol A	affects expression, decreases methylation	2
Benzo(a)pyrene	affects methylation, decreases methylation, increases methylation	2
Calcitriol	increases expression	2
Estradiol	decreases expression, affects cotreatment, increases expression	2
Progesterone	affects cotreatment, decreases expression	2
Smoke	increases expression	2
Tobacco Smoke Pollution	decreases expression	2
Tretinoin	decreases expression	2
Aflatoxin B1	increases methylation	2
Particulate Matter	decreases expression, increases abundance	2
propionaldehyde	increases expression	1
pirinixic acid	affects binding, increases activity, increases expression	1
methylselenic acid	increases expression	1
beta-lapachone	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
butyraldehyde	increases expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
nickel sulfate	increases expression	1
pentanal	increases expression	1
CGP 52608	affects binding, increases reaction	1
entinostat	increases expression	1
K 7174	increases expression	1
fenpyroximate	increases expression	1
jinfukang	increases expression	1
(+)-JQ1 compound	decreases expression	1
Temozolomide	decreases expression	1
Zoledronic Acid	increases expression	1
Arsenic Trioxide	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.