KHDC4

Chr 1

KH domain containing 4, pre-mRNA splicing factor

Also known as: BLOM7, KIAA0907, SNORA80EHG

NCBI Gene: 22889ENSG00000132680UniProt: Q7Z7F0

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]

ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant
This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.
0
Active trials
1
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.32
LOEUF· LoF intol.
LOF
Mechanism· predicted
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?
0.32LOEUF
pLI 0.969
Z-score 4.50
OE 0.15 (0.08–0.32)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?
1.74Z-score
OE missense 0.73 (0.66–0.81)
241 obs / 330.2 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.15 (0.08–0.32)
0≤0.351.4
Missense OE?0.73 (0.66–0.81)
0≤0.61.4
Synonymous OE?0.91
0≤1.21.6
LoF obs/exp: 5 / 32.8Missense obs/exp: 241 / 330.2Syn Z: 0.73

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

KHDC4 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients