PJVK

pejvakin, the group of Gasdermins

Basic information

Region (hg38): 2:178451346-178462102

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
autosomal recessive nonsyndromic hearing loss 59 (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 (188 variants)
Autosomal_recessive_nonsyndromic_hearing_loss_59 (50 variants)
Inborn_genetic_diseases (36 variants)
not_specified (22 variants)
PJVK-related_disorder (7 variants)
Deafness (4 variants)
Hearing_loss,_autosomal_recessive (4 variants)
Hearing_impairment (2 variants)
Rare_genetic_deafness (1 variants)
Ear_malformation (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. These statistics are base on transcript: NM_001042702.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous		1 clinvar	3 clinvar	71 clinvar		75
missense	4 clinvar	2 clinvar	66 clinvar	6 clinvar		78
nonsense	7 clinvar	6 clinvar				13
start loss			1			1
frameshift	16 clinvar	6 clinvar				22
splice donor/acceptor (+/-2bp)	2 clinvar	2 clinvar				4
Total	29	17	70	77	0

Highest pathogenic variant AF is 0.0000997543

Loading clinvar variants...

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

loftool
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_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap: N
gene_indispensability_pred
gene_indispensability_score

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);