JHY
protein-codingjunctional cadherin complex regulator
Gene summary
Predicted to be involved in axoneme assembly and brain development. Predicted to act upstream of or within several processes, including cerebrospinal fluid circulation; motile cilium assembly; and regulation of establishment of planar polarity. [provided by Alliance of Genome Resources, Jun 2026]
- C11orf63
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~81.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to JHY variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024806.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 7 | 1 | 8 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 8 | 2 | 0 | 10 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_079082.2 | 8 | MANE Select | |
| Ensembl | ENSP00000227349.2 | 8 | MANE Select | |
| RefSeq | NP_001350016.1 | 7 | Standard | |
| RefSeq | NP_001350017.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- brain development
- ciliary basal body organization
- cerebrospinal fluid secretion
- axoneme assembly
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000227349
- Coding exons
- 8
- Length
- 77116
- Individuals with no LoFs
- 125648
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 99
- Defined
- 125748
- p
- 0.000398
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.111 | 420 | 426 | 0.985 | 0.0000237 | 5139 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00075 | 0.00074 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0.00020 | 0.000099 | rare |
| East Asian | 0.00050 | 0.00049 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00042 | 0.00041 | rare |
| South Asian | 0.00059 | 0.00059 | rare |
| Other | 0.0016 | 0.0015 | notable |
dbNSFP Gene Annotations
Source:
- 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
Essentials
- Essential (gene trap)
- N