COL16A1

collagen type XVI alpha 1 chain, the group of Collagens

Basic information

Region (hg38): 1:31652262-31704319

Links

ENSG00000084636 ∙ NCBI:1307 ∙ OMIM:120326 ∙ HGNC:2193 ∙ Uniprot:Q07092 ∙ 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 COL16A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COL16A1 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				1		1
missense			90	5	2	97
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	90	6	3

Variants in COL16A1

This is a list of pathogenic ClinVar variants found in the COL16A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-31653644-T-C		not specified	Uncertain significance (Feb 10, 2022)
1-31653908-T-G		not specified	Uncertain significance (Jun 07, 2024)
1-31653980-C-A		not specified	Uncertain significance (Mar 14, 2023)
1-31655343-G-A		not specified	Uncertain significance (Jan 22, 2024)
1-31655425-C-G		not specified	Uncertain significance (Apr 12, 2022)
1-31655450-G-A		not specified	Uncertain significance (May 10, 2024)
1-31656405-G-T		not specified	Uncertain significance (Dec 05, 2022)
1-31658508-G-A		not specified	Uncertain significance (Jul 12, 2023)
1-31658552-G-A		not specified	Uncertain significance (Sep 29, 2023)
1-31658561-C-T		not specified	Uncertain significance (Dec 27, 2023)
1-31658916-C-A		not specified	Uncertain significance (Feb 02, 2024)
1-31658939-G-A		not specified	Uncertain significance (Nov 10, 2022)
1-31660595-G-A		not specified	Uncertain significance (Feb 06, 2024)
1-31660604-G-A		not specified	Uncertain significance (May 10, 2024)
1-31661661-G-A		not specified	Uncertain significance (Aug 02, 2023)
1-31661669-C-T		not specified	Uncertain significance (Aug 17, 2022)
1-31662337-C-G		not specified	Uncertain significance (Dec 20, 2023)
1-31662363-C-A		not specified	Uncertain significance (Jan 04, 2022)
1-31662622-C-G		not specified	Uncertain significance (Feb 12, 2024)
1-31662642-C-T		not specified	Uncertain significance (Dec 17, 2021)
1-31665194-G-A		not specified	Uncertain significance (Dec 17, 2023)
1-31665219-G-A		not specified	Uncertain significance (Feb 06, 2024)
1-31665887-C-T		not specified	Uncertain significance (Dec 13, 2023)
1-31666054-C-T		not specified	Uncertain significance (Apr 08, 2024)
1-31666066-C-T		not specified	Uncertain significance (Nov 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COL16A1	protein_coding	protein_coding	ENST00000373672	70	52073

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.90e-24	1.00	122387	125	2323	124835	0.00985

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	839	933	0.900	0.0000538	10007
Missense in Polyphen		51	69.274	0.73621		784
Synonymous	1.11	333	360	0.925	0.0000226	3409
Loss of Function	4.96	59	117	0.505	0.00000622	1323

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.137	0.135
Ashkenazi Jewish	0.00120	0.00119
East Asian	0.000733	0.000723
Finnish	0.00103	0.000974
European (Non-Finnish)	0.00163	0.00162
Middle Eastern	0.000733	0.000723
South Asian	0.00171	0.00164
Other	0.00579	0.00578

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in mediating cell attachment and inducing integrin-mediated cellular reactions, such as cell spreading and alterations in cell morphology. {ECO:0000269|PubMed:16754661}.
• Pathway: Collagen chain trimerization;Collagen biosynthesis and modifying enzymes;Integrin cell surface interactions;Collagen degradation;Collagen formation;Extracellular matrix organization;Integrin;Degradation of the extracellular matrix (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.132
• rvis_EVS: 0.58
• rvis_percentile_EVS: 82.18

Haploinsufficiency Scores

• pHI: 0.127
• hipred: N
• hipred_score: 0.414
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.742

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Col16a1

Gene ontology

• Biological process: cell adhesion;integrin-mediated signaling pathway;female pregnancy;extracellular matrix organization;integrin activation;cell adhesion mediated by integrin;positive regulation of focal adhesion assembly;cellular response to amino acid stimulus
• Cellular component: extracellular region;collagen type XVI trimer;extracellular space;endoplasmic reticulum lumen;extracellular matrix;collagen-containing extracellular matrix
• Molecular function: integrin binding;extracellular matrix structural constituent;protein binding;extracellular matrix structural constituent conferring tensile strength