COL14A1

collagen type XIV alpha 1 chain, the group of Fibronectin type III domain containing|Collagens

Basic information

Region (hg38): 8:120059780-120373573

Previous symbols: [ "UND" ]

Links

ENSG00000187955 ∙ NCBI:7373 ∙ OMIM:120324 ∙ HGNC:2191 ∙ Uniprot:Q05707 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• punctate palmoplantar keratoderma type 1 (Supportive), mode of inheritance: AD
• hereditary palmoplantar keratoderma (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COL14A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COL14A1 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				12	15	27
missense			73	14	8	95
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					4	4
non coding				2	72	74
Total	0	0	74	28	95

Variants in COL14A1

This is a list of pathogenic ClinVar variants found in the COL14A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-120147628-C-T			Benign (Nov 10, 2018)
8-120147858-C-T			Likely benign (Aug 28, 2018)
8-120147901-T-C		not specified	Likely benign (Nov 15, 2021)
8-120147909-T-A		not specified	Uncertain significance (May 29, 2024)
8-120157961-G-T			Benign (Nov 11, 2018)
8-120158145-G-A		not specified	Uncertain significance (Feb 12, 2024)
8-120158162-A-G		not specified	Uncertain significance (Aug 20, 2023)
8-120158188-A-G			Benign (Sep 08, 2018)
8-120158193-A-G		not specified	Uncertain significance (Mar 22, 2023)
8-120158564-G-A			Benign (Nov 11, 2018)
8-120162322-AT-A			Benign (Nov 10, 2018)
8-120162495-A-G			Benign (May 17, 2018)
8-120162528-A-G		not specified	Uncertain significance (Dec 08, 2023)
8-120162539-G-A		not specified	Uncertain significance (Nov 09, 2024)
8-120162562-A-G			Benign (May 18, 2018)
8-120162598-C-G			Benign (Nov 10, 2018)
8-120168161-T-C		not specified	Uncertain significance (Jun 07, 2024)
8-120168185-A-T		not specified	Uncertain significance (Jun 10, 2022)
8-120168425-G-A			Benign (Jun 18, 2021)
8-120168428-C-T			Benign (Nov 10, 2018)
8-120196761-A-C			Benign (Jun 18, 2021)
8-120196802-G-C			Benign (Jun 09, 2021)
8-120196878-G-C		not specified	Uncertain significance (Sep 14, 2022)
8-120196919-G-A		not specified	Likely benign (Dec 19, 2023)
8-120196924-G-A			Likely benign (Apr 30, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COL14A1	protein_coding	protein_coding	ENST00000297848	47	312257

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.43e-14	1.00	125649	0	99	125748	0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	843	979	0.861	0.0000513	11567
Missense in Polyphen		336	446.6	0.75236		5310
Synonymous	0.0110	356	356	0.999	0.0000203	3604
Loss of Function	5.47	42	102	0.414	0.00000554	1213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000763	0.000762
Ashkenazi Jewish	0.000408	0.000397
East Asian	0.000709	0.000653
Finnish	0.000187	0.000185
European (Non-Finnish)	0.000390	0.000378
Middle Eastern	0.000709	0.000653
South Asian	0.000526	0.000523
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an adhesive role by integrating collagen bundles. It is probably associated with the surface of interstitial collagen fibrils via COL1. The COL2 domain may then serve as a rigid arm which sticks out from the fibril and protrudes the large N-terminal globular domain into the extracellular space, where it might interact with other matrix molecules or cell surface receptors (By similarity). {ECO:0000250, ECO:0000269|PubMed:2187872}.
• Pathway: Protein digestion and absorption - Homo sapiens (human);Collagen chain trimerization;Collagen biosynthesis and modifying enzymes;Collagen degradation;Collagen formation;Extracellular matrix organization;Degradation of the extracellular matrix (Consensus)

Recessive Scores

• pRec: 0.186

Intolerance Scores

• loftool: 0.172
• rvis_EVS: -1.11
• rvis_percentile_EVS: 6.72

Haploinsufficiency Scores

• pHI: 0.155
• hipred: Y
• hipred_score: 0.602
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.699

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Col14a1
• Phenotype: skeleton phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); muscle phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: col14a1a
• Affected structure: dermis
• Phenotype tag: abnormal
• Phenotype quality: broken

Gene ontology

• Biological process: growth plate cartilage chondrocyte morphogenesis;extracellular matrix organization;collagen fibril organization;cell-cell adhesion
• Cellular component: extracellular region;collagen trimer;collagen type XIV trimer;extracellular space;endoplasmic reticulum lumen;extracellular matrix;collagen-containing extracellular matrix
• Molecular function: RNA binding;extracellular matrix structural constituent;collagen binding;extracellular matrix structural constituent conferring tensile strength;protein binding, bridging