COL19A1

collagen type XIX alpha 1 chain, the group of Collagens

Basic information

Region (hg38): 6:69866556-70212468

Links

ENSG00000082293 ∙ NCBI:1310 ∙ OMIM:120165 ∙ HGNC:2196 ∙ Uniprot:Q14993 ∙ 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 COL19A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COL19A1 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	4	5
missense			72	4	2	78
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					86	86
Total	0	0	72	5	92

Variants in COL19A1

This is a list of pathogenic ClinVar variants found in the COL19A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-69879619-C-A		not specified	Uncertain significance (Feb 12, 2024)
6-69879637-G-A		not specified	Uncertain significance (Feb 01, 2023)
6-69879738-G-C			Benign (Jun 18, 2021)
6-69879819-T-A			Benign (Jun 18, 2021)
6-69879831-A-G			Benign (Jun 18, 2021)
6-69899165-A-AT			Benign (Jun 19, 2021)
6-69899190-G-A			Benign (Jun 18, 2021)
6-69899263-C-G			Benign (Jun 18, 2021)
6-69900272-G-A		not specified	Likely benign (Dec 21, 2022)
6-69900391-C-T			Benign (Jun 18, 2021)
6-69929155-TAC-T			Benign (Jun 20, 2021)
6-69929155-T-TACACACACAC			Benign (Jun 20, 2021)
6-69929431-A-G		not specified	Likely benign (Dec 07, 2021)
6-69929488-G-A		not specified	Uncertain significance (Oct 13, 2023)
6-69929540-G-A		not specified	Uncertain significance (Mar 02, 2023)
6-69930005-A-T			Benign (Jun 18, 2021)
6-69932730-T-C			Benign (Jun 19, 2021)
6-69932768-C-T			Benign (Jun 18, 2021)
6-69932793-A-T		not specified	Uncertain significance (Aug 02, 2023)
6-69932816-G-T		not specified	Likely benign (Jul 17, 2023)
6-69932827-A-G		not specified	Uncertain significance (Mar 01, 2024)
6-69933126-A-G			Benign (Jun 18, 2021)
6-69936786-G-T		not specified	Uncertain significance (Jan 11, 2023)
6-69936867-C-G		not specified	Uncertain significance (May 07, 2024)
6-69936875-G-C		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COL19A1	protein_coding	protein_coding	ENST00000322773	50	343217

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.84e-33	0.0784	125538	0	210	125748	0.000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.327	609	632	0.963	0.0000323	7177
Missense in Polyphen		206	242.74	0.84863		2599
Synonymous	-0.415	210	203	1.04	0.0000103	2313
Loss of Function	2.12	62	82.8	0.749	0.00000417	1025

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00141	0.00141
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00130	0.00125
Finnish	0.000739	0.000739
European (Non-Finnish)	0.000878	0.000871
Middle Eastern	0.00130	0.00125
South Asian	0.00109	0.00108
Other	0.000491	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a cross-bridge between fibrils and other extracellular matrix molecules. Involved in skeletal myogenesis in the developing esophagus. May play a role in organization of the pericellular matrix or the sphinteric smooth muscle. {ECO:0000269|PubMed:12788917}.
• Pathway: Collagen chain trimerization;Collagen biosynthesis and modifying enzymes;Collagen formation;Extracellular matrix organization;Integrin (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.148
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.12

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.368

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0708

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Col19a1
• Phenotype: digestive/alimentary phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); muscle 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)

Zebrafish Information Network

• Gene name: col19a1
• Affected structure: CaP motoneuron
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: skeletal system development;cell adhesion;skeletal muscle tissue development;cell differentiation;extracellular matrix organization;collagen catabolic process;cell-cell adhesion
• Cellular component: extracellular region;collagen trimer;extracellular space;endoplasmic reticulum lumen;extracellular matrix
• Molecular function: extracellular matrix structural constituent;protein binding, bridging