COL26A1

protein-coding

collagen type XXVI alpha 1 chain, the group of EMI domain containing|Collagens

Gene summary

This gene encodes a protein containing an emilin domain and two collagen stretches. This gene may be associated with aspirin-intolerant asthma. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2013]

Previous symbols:

EMID2

MANE transcript

NM_001278563.3

Inheritance

—

ClinVar variants

U:69B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.52

Max pathogenic AF

—

Genomic locus

chr7:101,362,875-101,559,024

External References & Databases

Ensembl (ENSG00000160963)

Transcript & Mutation Effects

hg38 • Region Span ~196.1 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 COL26A1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 67

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001278563.3. 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			1 clinvar			1
missense			67 clinvar	2 clinvar		69
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	69	2	0	71

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001278563.3	RefSeq	NP_001265492.1	13	MANE Select
ENST00000313669.12	Ensembl	ENSP00000318234.8	13	MANE Select
NM_133457.5	RefSeq	NP_597714.2	13	Standard
ENST00000613501.1	Ensembl	ENSP00000482102.1	13	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 degradation
Collagen formation
Extracellular matrix organization

Biological Process

positive regulation of cell-substrate adhesion

Cellular Component

extracellular region
collagen trimer
endoplasmic reticulum lumen
Golgi apparatus
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: polymorphic_pseudogene
Transcript type: protein_coding
Transcript: ENST00000313669
Coding exons: 14
Length: 196204
Individuals with no LoFs: 1256
Homozygous LoFs: 123375
Heterozygous LoFs: 4
Defined: 124635
p: 0.900

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.184	247	255	0.968	0.0000153	2691
Missense (PolyPhen)		88	95.086	0.92548		948
Synonymous	-0.319	116	112	1.04	0.00000754	946
Loss of Function	2.20	13	24.8	0.523	0.00000154	247

Population LoF Frequency

Population	CAF	p-value	Status
African	1.0	0.93	notable
Latino/Admixed American	1.0	0.94	notable
Ashkenazi Jewish	1.0	0.93	notable
East Asian	1.0	0.97	notable
Finnish	1.0	0.97	notable
European (Non-Finnish)	1.0	0.86	notable
South Asian	1.0	0.95	notable
Other	1.0	0.92	notable

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR2): N