COL28A1

collagen type XXVIII alpha 1 chain, the group of Collagens

Basic information

Region (hg38): 7:7356202-7535873

Links

ENSG00000215018 ∙ NCBI:340267 ∙ OMIM:609996 ∙ HGNC:22442 ∙ Uniprot:Q2UY09 ∙ 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 COL28A1 gene.

• Inborn genetic diseases (57 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COL28A1 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				3	1	4
missense			56	2	1	59
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	56	5	2

Variants in COL28A1

This is a list of pathogenic ClinVar variants found in the COL28A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-7358651-T-A		not specified	Uncertain significance (Jun 29, 2022)
7-7358787-G-T		not specified	Uncertain significance (Sep 12, 2023)
7-7360398-C-T		not specified	Uncertain significance (Nov 21, 2022)
7-7360456-T-C		not specified	Uncertain significance (Mar 07, 2024)
7-7360483-G-A		not specified	Uncertain significance (Feb 28, 2023)
7-7370769-G-C		not specified	Uncertain significance (Dec 13, 2021)
7-7370798-T-A		not specified	Uncertain significance (Jul 05, 2023)
7-7370807-G-A		not specified	Uncertain significance (Feb 15, 2023)
7-7370825-A-C		not specified	Uncertain significance (Jan 04, 2024)
7-7370868-T-C		not specified	Uncertain significance (Jun 18, 2021)
7-7373261-T-A			Benign (Jul 25, 2017)
7-7373306-T-A		not specified	Uncertain significance (Aug 16, 2021)
7-7373306-T-C		not specified	Uncertain significance (May 30, 2022)
7-7373310-C-T		not specified	Uncertain significance (Dec 28, 2022)
7-7373313-C-T		not specified	Uncertain significance (Aug 12, 2021)
7-7373322-T-G		not specified	Uncertain significance (Jan 04, 2024)
7-7373367-C-T		not specified	Uncertain significance (May 22, 2023)
7-7373399-C-T		not specified	Uncertain significance (Apr 13, 2022)
7-7373426-C-T		not specified	Likely benign (May 27, 2022)
7-7373481-C-T		not specified	Uncertain significance (May 18, 2023)
7-7375487-A-C		not specified	Uncertain significance (Aug 21, 2023)
7-7380682-G-A		not specified	Uncertain significance (Oct 06, 2023)
7-7380698-A-G			Benign (Jul 25, 2017)
7-7380809-A-C		not specified	Uncertain significance (Feb 10, 2022)
7-7380819-T-G		not specified	Uncertain significance (Jul 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COL28A1	protein_coding	protein_coding	ENST00000399429	34	179651

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.68e-32	0.00271	123618	7	1169	124794	0.00472

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.879	678	617	1.10	0.0000316	7177
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0292	0.0292
Ashkenazi Jewish	0.00358	0.00358
East Asian	0.00101	0.00100
Finnish	0.0000939	0.0000928
European (Non-Finnish)	0.000855	0.000848
Middle Eastern	0.00101	0.00100
South Asian	0.00235	0.00229
Other	0.00545	0.00546

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a cell-binding protein.
• Pathway: Collagen chain trimerization;Collagen biosynthesis and modifying enzymes;Collagen formation;Extracellular matrix organization (Consensus)

Intolerance Scores

• loftool: 0.160
• rvis_EVS: 2.04
• rvis_percentile_EVS: 97.73

Haploinsufficiency Scores

• pHI: 0.189
• hipred: N
• hipred_score: 0.167
• ghis: 0.435

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.143

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Col28a1

Gene ontology

• Biological process: cell adhesion;negative regulation of endopeptidase activity;extracellular matrix organization
• Cellular component: extracellular region;collagen trimer;basement membrane;extracellular space;endoplasmic reticulum lumen;extracellular matrix;collagen-containing extracellular matrix
• Molecular function: serine-type endopeptidase inhibitor activity;extracellular matrix structural constituent;extracellular matrix structural constituent conferring tensile strength