PJVK

pejvakin, the group of Gasdermins

Basic information

Region (hg38): 2:178451345-178462102

Previous symbols: [ "DFNB59" ]

Links

ENSG00000204311 ∙ NCBI:494513 ∙ OMIM:610219 ∙ HGNC:29502 ∙ Uniprot:Q0ZLH3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
• autosomal recessive nonsyndromic hearing loss 59 (Strong), mode of inheritance: AR
• nonsyndromic genetic hearing loss (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal recessive 59	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic	17718865; 17373699; 7301963; 17329413

ClinVar

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

• not provided (111 variants)
• Autosomal recessive nonsyndromic hearing loss 59 (46 variants)
• not specified (25 variants)
• Nonsyndromic Hearing Loss, Recessive (3 variants)
• Hearing impairment (2 variants)
• Deafness (1 variants)
• Ear malformation (1 variants)
• Hearing loss, autosomal recessive (1 variants)
• Dystonic disorder (1 variants)
• Inborn genetic diseases (1 variants)
• Rare genetic deafness (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PJVK 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			5	24		29
missense	4		34	4		42
nonsense	5	2				7
start loss			1			1
frameshift	5					5
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region		1		3		4
non coding			15	26	12	53
Total	14	2	56	54	12

Highest pathogenic variant AF is 0.0000394

Variants in PJVK

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

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

Position	Type	Phenotype	Significance	ClinVar
2-178451489-G-A		Nonsyndromic Hearing Loss, Recessive • Autosomal recessive nonsyndromic hearing loss 59	Uncertain significance (Jan 13, 2018)
2-178451509-C-G		Autosomal recessive nonsyndromic hearing loss 59	Uncertain significance (Jan 13, 2018)
2-178451529-G-A		Nonsyndromic Hearing Loss, Recessive • Autosomal recessive nonsyndromic hearing loss 59	Uncertain significance (Jan 13, 2018)
2-178451558-C-T		Autosomal recessive nonsyndromic hearing loss 59	Uncertain significance (Jan 13, 2018)
2-178451560-A-G		Autosomal recessive nonsyndromic hearing loss 59	Uncertain significance (Jan 13, 2018)
2-178451591-C-G		Autosomal recessive nonsyndromic hearing loss 59	Uncertain significance (Jan 13, 2018)
2-178451668-G-A		Autosomal recessive nonsyndromic hearing loss 59	Uncertain significance (Jan 13, 2018)
2-178451680-G-T		Autosomal recessive nonsyndromic hearing loss 59	Uncertain significance (Jan 12, 2018)
2-178451708-C-T		Autosomal recessive nonsyndromic hearing loss 59	Uncertain significance (Jan 13, 2018)
2-178451710-C-T		Autosomal recessive nonsyndromic hearing loss 59	Uncertain significance (Jan 13, 2018)
2-178451719-C-T		Autosomal recessive nonsyndromic hearing loss 59	Uncertain significance (Jan 13, 2018)
2-178451728-C-T		Autosomal recessive nonsyndromic hearing loss 59	Uncertain significance (Jan 13, 2018)
2-178451743-G-T		Autosomal recessive nonsyndromic hearing loss 59	Uncertain significance (Jan 13, 2018)
2-178451747-T-A		Nonsyndromic Hearing Loss, Recessive • Autosomal recessive nonsyndromic hearing loss 59	Uncertain significance (Jan 12, 2018)
2-178451764-C-G		Dystonic disorder • Autosomal recessive nonsyndromic hearing loss 59	Likely benign (Jan 13, 2018)
2-178453333-C-T			Likely benign (Apr 12, 2019)
2-178453382-T-A		Autosomal recessive nonsyndromic hearing loss 59	Conflicting classifications of pathogenicity (Jun 16, 2020)
2-178453410-A-G		not specified	Uncertain significance (Jun 01, 2020)
2-178453427-C-G			Likely benign (Dec 10, 2023)
2-178453442-G-A			Likely benign (Jul 25, 2023)
2-178453458-G-A			Uncertain significance (Apr 25, 2016)
2-178453462-G-T		not specified	Uncertain significance (Dec 19, 2012)
2-178453465-T-G			Pathogenic (Jun 20, 2023)
2-178453495-A-G		not specified • Autosomal recessive nonsyndromic hearing loss 59 • PJVK-related disorder	Conflicting classifications of pathogenicity (Jan 30, 2024)
2-178453496-C-A			Likely benign (Jan 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PJVK	protein_coding	protein_coding	ENST00000409117	6	9955

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.72e-8	0.568	124818	0	60	124878	0.000240

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.134	181	186	0.972	0.00000919	2286
Missense in Polyphen		58	59.773	0.97034		775
Synonymous	0.774	57	64.9	0.878	0.00000309	686
Loss of Function	1.07	14	19.1	0.735	0.00000140	204

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000569	0.000568
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.000389	0.000388
Finnish	0.00	0.00
European (Non-Finnish)	0.000274	0.000274
Middle Eastern	0.000389	0.000388
South Asian	0.000295	0.000261
Other	0.000330	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential in the activity of auditory pathway neurons.

Intolerance Scores

• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.377
• hipred: N
• hipred_score: 0.254
• ghis: 0.518

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Pjvk
• Phenotype: hearing/vestibular/ear phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)