COL28A1

protein-coding

collagen type XXVIII alpha 1 chain, the group of Collagens

Gene summary

COL28A1 belongs to a class of collagens containing von Willebrand factor (VWF; MIM 613160) type A (VWFA) domains (Veit et al., 2006 [PubMed 16330543]).[supplied by OMIM, Nov 2010]

MANE transcript

NM_001037763.3

Inheritance

—

ClinVar variants

U:196B:13

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.83

Max pathogenic AF

—

Genomic locus

chr7:7,356,203-7,535,873

External References & Databases

Ensembl (ENSG00000215018)

Transcript & Mutation Effects

hg38 • Region Span ~179.7 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 COL28A1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 186

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001037763.3. 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			2 clinvar	3 clinvar	1 clinvar	6
missense			183 clinvar	8 clinvar	1 clinvar	192
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	196	11	2	209

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001037763.3	RefSeq	NP_001032852.2	34	MANE Select
ENST00000399429.8	Ensembl	ENSP00000382356.3	34	MANE Select
ENST00000430711.5	Ensembl	ENSP00000413093.1	3	Standard
ENST00000435823.1	Ensembl	ENSP00000410557.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Collagen chain trimerization
Collagen biosynthesis and modifying enzymes
Collagen formation
Extracellular matrix organization

Biological Process

cell adhesion
negative regulation of endopeptidase activity
extracellular matrix organization

Molecular Function

serine-type endopeptidase inhibitor activity
extracellular matrix structural constituent
extracellular matrix structural constituent conferring tensile strength

Cellular Component

extracellular region
collagen trimer
basement membrane
extracellular space
endoplasmic reticulum lumen

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000399429
Coding exons: 34
Length: 179651
Individuals with no LoFs: 123618
Homozygous LoFs: 7
Heterozygous LoFs: 1169
Defined: 124794
p: 0.00472

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.879	678	617	1.10	0.0000316	7177
Missense (PolyPhen)		310	281.73	1.1003		3173
Synonymous	-1.79	246	213	1.16	0.0000114	2261
Loss of Function	1.29	55	66.3	0.829	0.00000320	838

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0042	0.0042	notable
Latino/Admixed American	0.025	0.025	notable
Ashkenazi Jewish	0.0036	0.0036	notable
East Asian	0.0010	0.0010	notable
Finnish	0.000094	0.000093	rare
European (Non-Finnish)	0.00085	0.00085	rare
South Asian	0.0023	0.0023	notable
Other	0.0055	0.0055	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as a cell-binding protein.;

Intolerance Scores

LoFtool: 0.160
RVIS EVS: 2.04
RVIS percentile EVS: 97.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.143

Gene Damage Prediction

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