KHDC4
protein-codingKH domain containing 4, pre-mRNA splicing factor, the group of Small nucleolar RNA protein coding host genes
Gene summary
Enables RNA binding activity. Involved in mRNA splice site recognition. Located in cytoplasm; nucleoplasm; and spliceosomal complex. [provided by Alliance of Genome Resources, Jul 2025]
- KIAA0907
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~21.4 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 KHDC4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014949.4. 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 | 2 | 1 | 3 | |||
| missense | 79 | 79 | ||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 85 | 1 | 0 | 86 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055764.2 | 14 | MANE Select | |
| Ensembl | ENSP00000357304.3 | 14 | MANE Select | |
| Ensembl | ENSP00000357302.3 | 10 | Standard | |
| Ensembl | ENSP00000357303.3 | 13 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- mRNA splice site selection
Molecular Function
- RNA binding
- protein binding
Cellular Component
- nucleus
- spliceosomal complex
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000368321
- Coding exons
- 14
- Length
- 21358
- Individuals with no LoFs
- 125738
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 10
- Defined
- 125748
- p
- 0.0000398
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.74 | 241 | 330 | 0.730 | 0.0000161 | 3925 |
| Missense (PolyPhen) | 58 | 119.57 | 0.48507 | 1399 | ||
| Synonymous | 0.733 | 107 | 117 | 0.914 | 0.00000569 | 1274 |
| Loss of Function | 4.50 | 5 | 32.8 | 0.152 | 0.00000179 | 374 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.00028 | 0.00028 | rare |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: RNA-binding protein involved in pre-mRNA splicing (PubMed:19641227). Interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome (PubMed:19641227). Involved in regulating splice site selection (PubMed:19641227). Binds preferentially RNA with A/C rich sequences and poly-C stretches (PubMed:23144703). {ECO:0000269|PubMed:19641227, ECO:0000269|PubMed:23144703}.;
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- RVIS EVS
- -0.58
- RVIS percentile EVS
- 18.44
Essentials
- Essential (gene trap)
- N