COL21A1

protein-coding

collagen type XXI alpha 1 chain, the group of Collagens

Gene summary

This gene encodes the alpha chain of type XXI collagen, a member of the FACIT (fibril-associated collagens with interrupted helices) collagen family. Type XXI collagen is localized to tissues containing type I collagen and maintains the integrity of the extracellular matrix. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

MANE transcript

NM_030820.4

Inheritance

—

ClinVar variants

U:141B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr6:56,056,590-56,394,094

External References & Databases

Ensembl (ENSG00000124749)

Transcript & Mutation Effects

hg38 • Region Span ~337.5 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 COL21A1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 128

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030820.4. 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			2 clinvar	2 clinvar	1 clinvar	5
missense			133 clinvar	7 clinvar	1 clinvar	141
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	141	9	2	152

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030820.4	RefSeq	NP_110447.2	29	MANE Select
ENST00000244728.10	Ensembl	ENSP00000244728.5	29	MANE Select
NM_001318751.2	RefSeq	NP_001305680.1	29	Standard
NM_001318752.2	RefSeq	NP_001305681.1	28	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Protein digestion and absorption - Homo sapiens (human)
Proteoglycans in cancer - Homo sapiens (human)
Type 2 papillary renal cell carcinoma
Collagen chain trimerization
Collagen biosynthesis and modifying enzymes

Biological Process

growth plate cartilage chondrocyte morphogenesis

Molecular Function

extracellular matrix structural constituent conferring tensile strength

Cellular Component

extracellular region
collagen trimer
extracellular space
endoplasmic reticulum lumen
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000244728
Coding exons: 29
Length: 337505
Individuals with no LoFs: 124220
Homozygous LoFs: 0
Heterozygous LoFs: 422
Defined: 124642
p: 0.00169

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.809	421	470	0.895	0.0000234	5995
Missense (PolyPhen)		145	181.31	0.79973		2165
Synonymous	-1.13	182	164	1.11	0.00000859	1908
Loss of Function	1.52	43	55.1	0.780	0.00000297	742

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0060	0.0055	notable
Latino/Admixed American	0.0019	0.0018	notable
Ashkenazi Jewish	0.00041	0.00040	rare
East Asian	0.010	0.0098	notable
Finnish	0.00061	0.00060	rare
European (Non-Finnish)	0.00054	0.00052	rare
South Asian	0.00058	0.00056	rare
Other	0.0012	0.0012	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.136

Intolerance Scores

LoFtool: 0.0800
RVIS EVS: 0.72
RVIS percentile EVS: 85.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.230

Gene Damage Prediction

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