COL26A1

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

Basic information

Region (hg38): 7:101362874-101559024

Previous symbols: [ "EMID2" ]

Links

ENSG00000160963 ∙ NCBI:136227 ∙ OMIM:608927 ∙ HGNC:18038 ∙ Uniprot:Q96A83 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COL26A1 gene.

• Inborn genetic diseases (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COL26A1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in COL26A1

This is a list of pathogenic ClinVar variants found in the COL26A1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-101363060-G-A		not specified	Uncertain significance (Dec 02, 2022)
7-101363138-G-A		not specified	Uncertain significance (Mar 07, 2023)
7-101363138-G-C		not specified	Uncertain significance (Jun 28, 2023)
7-101363181-C-G		not specified	Uncertain significance (Feb 03, 2022)
7-101420039-C-T		not specified	Uncertain significance (Apr 12, 2022)
7-101447692-C-T		not specified	Uncertain significance (May 04, 2022)
7-101447728-C-T		not specified	Uncertain significance (May 06, 2022)
7-101533121-G-A		not specified	Uncertain significance (Feb 27, 2024)
7-101539966-C-T		not specified	Uncertain significance (Sep 14, 2023)
7-101540008-C-T		not specified	Uncertain significance (Dec 15, 2022)
7-101540023-G-T		not specified	Uncertain significance (Jun 06, 2023)
7-101540037-A-C		not specified	Uncertain significance (Mar 04, 2024)
7-101540038-C-T		not specified	Uncertain significance (Oct 13, 2023)
7-101544000-C-T		not specified	Uncertain significance (Jun 07, 2023)
7-101544004-C-T		not specified	Uncertain significance (Oct 20, 2023)
7-101544030-G-C		not specified	Uncertain significance (Sep 25, 2023)
7-101544039-C-G		not specified	Uncertain significance (Mar 01, 2023)
7-101544067-C-G		not specified	Uncertain significance (Jun 10, 2022)
7-101544091-C-T		not specified	Uncertain significance (Jan 17, 2024)
7-101545353-C-T		not specified	Uncertain significance (Feb 07, 2023)
7-101545359-C-T		not specified	Uncertain significance (Feb 15, 2023)
7-101545388-C-T		not specified	Uncertain significance (Aug 17, 2022)
7-101545473-C-T		not specified	Uncertain significance (Dec 21, 2023)
7-101547161-G-A		not specified	Uncertain significance (Jan 05, 2022)
7-101547224-C-A		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COL26A1	polymorphic_pseudogene	protein_coding	ENST00000313669	14	196204

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000293	0.985	1256	123375	4	124635	0.900

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.184	247	255	0.968	0.0000153	2691
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	2.00	1.93
Ashkenazi Jewish	1.00	0.932
East Asian	1.00	0.965
Finnish	1.00	0.965
European (Non-Finnish)	1.00	0.863
Middle Eastern	1.00	0.965
South Asian	1.00	0.954
Other	1.00	0.921

dbNSFP

Source: dbNSFP

• Pathway: Collagen chain trimerization;Collagen biosynthesis and modifying enzymes;Collagen degradation;Collagen formation;Extracellular matrix organization;Degradation of the extracellular matrix (Consensus)

Haploinsufficiency Scores

• pHI: 0.192
• hipred: N
• hipred_score: 0.288

Essentials

• essential_gene_CRISPR2: N

Mouse Genome Informatics

• Gene name: Col26a1

Gene ontology

• Biological process: positive regulation of cell-substrate adhesion
• Cellular component: extracellular region;collagen trimer;endoplasmic reticulum lumen;Golgi apparatus;plasma membrane;extracellular matrix;collagen-containing extracellular matrix