OVCH1

ovochymase 1

Basic information

Region (hg38): 12:29412474-29497686

Links

ENSG00000187950 ∙ NCBI:341350 ∙ ∙ HGNC:23080 ∙ Uniprot:Q7RTY7 ∙ 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 OVCH1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OVCH1 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						0
missense			60	5		65
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	60	5	0

Variants in OVCH1

This is a list of pathogenic ClinVar variants found in the OVCH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-29433785-C-G		not specified	Uncertain significance (Oct 14, 2023)
12-29443399-C-T		not specified	Likely benign (Jun 03, 2022)
12-29443418-C-G		not specified	Uncertain significance (Nov 03, 2022)
12-29443438-G-A		not specified	Uncertain significance (Feb 22, 2023)
12-29443462-A-G		not specified	Uncertain significance (Nov 17, 2022)
12-29443469-G-A		not specified	Uncertain significance (Oct 05, 2021)
12-29443474-A-G		not specified	Uncertain significance (Apr 08, 2024)
12-29444161-G-A		not specified	Uncertain significance (Nov 27, 2023)
12-29444226-A-G		not specified	Uncertain significance (Feb 15, 2023)
12-29444229-T-G		not specified	Uncertain significance (Sep 22, 2023)
12-29445308-C-T		not specified	Uncertain significance (Jun 05, 2024)
12-29445388-C-T		not specified	Uncertain significance (Dec 16, 2022)
12-29451488-A-G		not specified	Uncertain significance (Jan 07, 2022)
12-29451489-G-C		not specified	Uncertain significance (Jan 06, 2023)
12-29451515-C-T		not specified	Uncertain significance (Nov 29, 2023)
12-29454873-G-C		not specified	Uncertain significance (Dec 20, 2021)
12-29454897-G-T		not specified	Uncertain significance (Apr 17, 2024)
12-29455251-T-C		not specified	Uncertain significance (Mar 29, 2024)
12-29455258-T-C		not specified	Uncertain significance (May 14, 2024)
12-29455293-G-T		not specified	Uncertain significance (May 30, 2023)
12-29455312-A-G		not specified	Likely benign (Apr 23, 2024)
12-29461868-T-C		not specified	Uncertain significance (Sep 22, 2022)
12-29461922-G-A		not specified	Uncertain significance (Sep 01, 2021)
12-29461940-T-C		not specified	Uncertain significance (Sep 09, 2021)
12-29464521-C-T		not specified	Uncertain significance (Jan 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OVCH1	protein_coding	protein_coding	ENST00000318184	28	85213

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.94e-36	0.0000124	124308	2	484	124794	0.00195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.383	543	569	0.955	0.0000275	7342
Missense in Polyphen		107	122.45	0.87382		1680
Synonymous	0.185	202	205	0.984	0.0000108	2140
Loss of Function	0.160	55	56.3	0.977	0.00000256	769

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00411	0.00410
Ashkenazi Jewish	0.000304	0.000298
East Asian	0.00561	0.00530
Finnish	0.00392	0.00367
European (Non-Finnish)	0.00185	0.00180
Middle Eastern	0.00561	0.00530
South Asian	0.000417	0.000392
Other	0.00119	0.00115

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.0580
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0521

Gene Damage Prediction

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

Gene ontology

• Biological process: proteolysis
• Cellular component: extracellular region
• Molecular function: serine-type endopeptidase activity;metal ion binding