COL16A1

protein-coding

collagen type XVI alpha 1 chain, the group of Collagens

Gene summary

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. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001856.4

Inheritance

—

ClinVar variants

U:294B:16

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr1:31,652,263-31,704,319

External References & Databases

Ensembl (ENSG00000084636)

Transcript & Mutation Effects

hg38 • Region Span ~52.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to COL16A1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 250

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001856.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			13 clinvar	2 clinvar		15
missense			246 clinvar	13 clinvar	1 clinvar	260
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			32 clinvar			32
Total	0	0	294	15	1	310

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001856.4	RefSeq	NP_001847.3	70	MANE Select
ENST00000373672.8	Ensembl	ENSP00000362776.3	70	MANE Select
ENST00000373667.4	Ensembl	ENSP00000362771.4	17	Standard
ENST00000373668.7	Ensembl	ENSP00000362772.3	40	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Collagen chain trimerization
Collagen biosynthesis and modifying enzymes
Integrin cell surface interactions
Collagen degradation
Collagen formation

Biological Process

cell adhesion
integrin-mediated signaling pathway
female pregnancy
extracellular matrix organization
integrin activation

Molecular Function

integrin binding
extracellular matrix structural constituent
protein binding
extracellular matrix structural constituent conferring tensile strength

Cellular Component

extracellular region
collagen type XVI trimer
extracellular space
endoplasmic reticulum lumen
extracellular matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373672
Coding exons: 70
Length: 52073
Individuals with no LoFs: 122387
Homozygous LoFs: 125
Heterozygous LoFs: 2323
Defined: 124835
p: 0.00985

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.09	839	933	0.900	0.0000538	10007
Missense (PolyPhen)		51	69.274	0.73621		784
Synonymous	1.11	333	360	0.925	0.0000226	3409
Loss of Function	4.96	59	117	0.505	0.00000622	1323

Population LoF Frequency

Population	CAF	p-value	Status
African	0.13	0.13	notable
Latino/Admixed American	0.0085	0.0085	notable
Ashkenazi Jewish	0.0012	0.0012	notable
East Asian	0.00073	0.00072	rare
Finnish	0.0010	0.00097	notable
European (Non-Finnish)	0.0016	0.0016	notable
South Asian	0.0017	0.0016	notable
Other	0.0058	0.0058	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in mediating cell attachment and inducing integrin-mediated cellular reactions, such as cell spreading and alterations in cell morphology. {ECO:0000269|PubMed:16754661}.;

Recessive Scores

pRec: 0.127

Intolerance Scores

LoFtool: 0.132
RVIS EVS: 0.58
RVIS percentile EVS: 82.18

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.742

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium