COL17A1

collagen type XVII alpha 1 chain, the group of Collagens|MicroRNA protein coding host genes

Basic information

Region (hg38): 10:104031286-104085880

Previous symbols: [ "BPAG2" ]

Links

ENSG00000065618 ∙ NCBI:1308 ∙ OMIM:113811 ∙ HGNC:2194 ∙ Uniprot:Q9UMD9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• junctional epidermolysis bullosa, non-Herlitz type (Strong), mode of inheritance: AR
• junctional epidermolysis bullosa, non-Herlitz type (Definitive), mode of inheritance: AR
• epithelial recurrent erosion dystrophy (Moderate), mode of inheritance: AD
• epithelial recurrent erosion dystrophy (Strong), mode of inheritance: AD
• junctional epidermolysis bullosa, non-Herlitz type (Strong), mode of inheritance: AR
• generalized junctional epidermolysis bullosa non-Herlitz type (Supportive), mode of inheritance: AR
• late-onset junctional epidermolysis bullosa (Supportive), mode of inheritance: AR
• localized junctional epidermolysis bullosa, non-Herlitz type (Supportive), mode of inheritance: AR
• epithelial recurrent erosion dystrophy (Supportive), mode of inheritance: AD
• epithelial recurrent erosion dystrophy (Strong), mode of inheritance: AD
• junctional epidermolysis bullosa, non-Herlitz type (Strong), mode of inheritance: AR
• epithelial recurrent erosion dystrophy (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Epithelial recurrent erosion dystrophy; Epidermolysis bullosa, junctional 4, intermediate	AD/AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic; Ophthalmologic	2663347; 7883981; 7550320; 9038345; 9403072; 17263807; 17596158; 19369679; 20301304; 21357940; 21466533; 22965308; 25676728

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COL17A1 gene.

• not provided (71 variants)
• Junctional epidermolysis bullosa (7 variants)
• Epidermolysis bullosa, junctional 4, intermediate (7 variants)
• Epithelial recurrent erosion dystrophy (5 variants)
• Junctional epidermolysis bullosa, non-Herlitz type (4 variants)
• Amelogenesis imperfecta type 1A (3 variants)
• COL17A1-related disorder (2 variants)
• 14 conditions (1 variants)
• Corneal dystrophy (1 variants)
• Amelogenesis imperfecta (1 variants)
• Inborn genetic diseases (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COL17A1 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	2		2	358	15	377
missense	4	3	159	26	17	209
nonsense	32	5	1	1		39
start loss						0
frameshift	35	9				44
inframe indel		1	1	2		4
splice donor/acceptor (+/-2bp)	10	39	1			50
splice region		1	8	105	3	117
non coding			15	378	125	518
Total	83	57	179	765	157

Highest pathogenic variant AF is 0.0000594

Variants in COL17A1

This is a list of pathogenic ClinVar variants found in the COL17A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-104031288-T-C		Junctional epidermolysis bullosa	Uncertain significance (Jun 14, 2016)
10-104031412-A-C		Junctional epidermolysis bullosa, non-Herlitz type	Uncertain significance (Jan 13, 2018)
10-104031485-GT-G		Junctional epidermolysis bullosa	Likely benign (Jun 14, 2016)
10-104031491-C-A		Junctional epidermolysis bullosa, non-Herlitz type	Uncertain significance (Jan 12, 2018)
10-104031597-C-T		Junctional epidermolysis bullosa, non-Herlitz type	Benign (Jan 12, 2018)
10-104031677-C-G		Junctional epidermolysis bullosa, non-Herlitz type	Uncertain significance (Jan 13, 2018)
10-104031808-C-T		Junctional epidermolysis bullosa, non-Herlitz type	Uncertain significance (Jan 22, 2018)
10-104031841-G-T		Junctional epidermolysis bullosa, non-Herlitz type	Uncertain significance (Jan 13, 2018)
10-104031858-C-T		Junctional epidermolysis bullosa, non-Herlitz type	Uncertain significance (Jan 12, 2018)
10-104031859-G-A		Junctional epidermolysis bullosa, non-Herlitz type	Uncertain significance (Jan 12, 2018)
10-104031871-CA-C		Junctional epidermolysis bullosa	Benign (Jun 14, 2016)
10-104031874-A-G		Junctional epidermolysis bullosa, non-Herlitz type	Uncertain significance (Jan 13, 2018)
10-104032112-A-G		Junctional epidermolysis bullosa, non-Herlitz type	Uncertain significance (Jan 13, 2018)
10-104032120-T-C		Junctional epidermolysis bullosa, non-Herlitz type	Uncertain significance (Jan 13, 2018)
10-104032161-C-A		Junctional epidermolysis bullosa, non-Herlitz type	Benign (Jan 12, 2018)
10-104032171-C-G		Junctional epidermolysis bullosa, non-Herlitz type	Benign (Nov 10, 2018)
10-104032178-C-T		Junctional epidermolysis bullosa, non-Herlitz type	Uncertain significance (Jan 13, 2018)
10-104032227-T-C		Junctional epidermolysis bullosa, non-Herlitz type • COL17A1-related disorder	Likely benign (Jan 13, 2018)
10-104032230-C-G		COL17A1-related disorder	Likely benign (Jan 19, 2024)
10-104032238-C-T			Likely benign (Nov 27, 2023)
10-104032244-G-A			Likely benign (Apr 11, 2023)
10-104032247-A-G			Likely benign (Nov 28, 2023)
10-104032253-ACTT-A			Uncertain significance (Jan 08, 2024)
10-104032256-T-A		Inborn genetic diseases	Uncertain significance (Apr 10, 2023)
10-104032269-C-T			Uncertain significance (Sep 23, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COL17A1	protein_coding	protein_coding	ENST00000353479	55	54717

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.29e-27	1.00	125513	0	235	125748	0.000935

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.748	920	858	1.07	0.0000509	9419
Missense in Polyphen		206	203.54	1.0121		2033
Synonymous	-0.289	338	331	1.02	0.0000214	3217
Loss of Function	3.63	59	97.7	0.604	0.00000586	1068

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00251	0.00251
Ashkenazi Jewish	0.00437	0.00437
East Asian	0.000711	0.000707
Finnish	0.000652	0.000647
European (Non-Finnish)	0.000670	0.000659
Middle Eastern	0.000711	0.000707
South Asian	0.000892	0.000850
Other	0.00147	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the integrity of hemidesmosome and the attachment of basal keratinocytes to the underlying basement membrane.
• Disease: DISEASE: Generalized atrophic benign epidermolysis bullosa (GABEB) [MIM:226650]: A non-lethal, adult form of junctional epidermolysis bullosa characterized by life-long blistering of the skin, associated with hair and tooth abnormalities. {ECO:0000269|PubMed:10652291, ECO:0000269|PubMed:10951237, ECO:0000269|PubMed:11912005, ECO:0000269|PubMed:8669466, ECO:0000269|PubMed:9199555}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epithelial recurrent erosion dystrophy (ERED) [MIM:122400]: A corneal dystrophy characterized by recurrent episodes of epithelial erosions from childhood, with occasional impairment of vision. Most patients have attacks of redness, photophobia, epiphora, and ocular pain. Exposure to sunlight or draught, dust and smoke and lack of sleep can precipitate attacks. {ECO:0000269|PubMed:25676728}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Protein digestion and absorption - Homo sapiens (human);Collagen chain trimerization;Collagen biosynthesis and modifying enzymes;Alpha6Beta4Integrin;Collagen degradation;Collagen formation;Extracellular matrix organization;EGFR1;Degradation of the extracellular matrix;a6b1 and a6b4 Integrin signaling;Type I hemidesmosome assembly;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.283

Intolerance Scores

• loftool: 0.104
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.58

Haploinsufficiency Scores

• pHI: 0.253
• hipred: Y
• hipred_score: 0.628
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.407

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Col17a1
• 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); growth/size/body region phenotype; cellular phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); pigmentation phenotype; 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); reproductive system phenotype; hematopoietic system phenotype; renal/urinary system phenotype

Zebrafish Information Network

• Gene name: col17a1a
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: distended

Gene ontology

• Biological process: cell-matrix adhesion;epidermis development;extracellular matrix organization;hemidesmosome assembly;regulation of immune response
• Cellular component: extracellular region;collagen trimer;basement membrane;extracellular space;endoplasmic reticulum lumen;plasma membrane;integral component of plasma membrane;cell-cell junction;hemidesmosome;extracellular matrix;collagen-containing extracellular matrix
• Molecular function: extracellular matrix structural constituent;protein binding;extracellular matrix structural constituent conferring tensile strength