JHY

junctional cadherin complex regulator

Basic information

Region (hg38): 11:122882683-122963862

Previous symbols: [ "C11orf63" ]

Links

ENSG00000109944 ∙ NCBI:79864 ∙ OMIM:617594 ∙ HGNC:26288 ∙ Uniprot:Q6NUN7 ∙ 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 JHY gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JHY 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		1
missense			3	1		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	2	0

Variants in JHY

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

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

Position	Type	Phenotype	Significance	ClinVar
11-122904019-T-C			Likely benign (Dec 01, 2022)
11-122904316-C-T		not specified	Uncertain significance (Nov 16, 2021)
11-122946550-T-C		not specified	Likely benign (Oct 22, 2021)
11-122959256-A-T		not specified	Uncertain significance (Jun 18, 2021)
11-122959365-T-A		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JHY	protein_coding	protein_coding	ENST00000227349	8	77116

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.93e-12	0.886	125648	1	99	125748	0.000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.111	420	426	0.985	0.0000237	5139
Missense in Polyphen		86	95.084	0.90446		1266
Synonymous	0.198	165	168	0.981	0.0000105	1432
Loss of Function	1.94	24	36.7	0.654	0.00000184	450

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000833	0.000825
Ashkenazi Jewish	0.000198	0.0000992
East Asian	0.000496	0.000489
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000415	0.000413
Middle Eastern	0.000496	0.000489
South Asian	0.000588	0.000588
Other	0.00164	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for the normal development of cilia in brain ependymal cells lining the ventricular surfaces. {ECO:0000250|UniProtKB:E9Q793}.

Intolerance Scores

• rvis_EVS: -1.28
• rvis_percentile_EVS: 5.11

Haploinsufficiency Scores

• pHI: 0.0732
• hipred: N
• hipred_score: 0.123
• ghis: 0.518

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Jhy
• 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; cellular phenotype; growth/size/body region phenotype; craniofacial phenotype

Gene ontology

• Biological process: brain development;ciliary basal body organization;cerebrospinal fluid secretion;axoneme assembly