CHTOP

Chr 1

chromatin target of PRMT1

Also known as: C10orf77, C1orf77, FL-SRAG, FOP, SRAG, SRAG-3, SRAG-5, pp7704

NCBI Gene: 26097ENSG00000160679UniProt: Q9Y3Y2

This gene encodes a small nuclear protein that is characterized by an arginine and glycine rich region. This protein may have an important role in the regulation of fetal globin gene expression and in the activation of estrogen-responsive genes. A recent study reported that this protein binds 5-hydroxymethylcytosine (5hmC) and associates with an arginine methyltransferase complex (methylosome), which promotes methylation of arginine 3 of histone H4 (H4R3) and activation of genes involved in glioblastomagenesis. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Nov 2015]

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
3
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.43
LOEUF
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
Moderate LoF intolerance
LoF Constraint?
0.43LOEUF
pLI 0.764
Z-score 3.27
OE 0.17 (0.07–0.43)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?
1.70Z-score
OE missense 0.63 (0.54–0.74)
105 obs / 166.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.17 (0.07–0.43)
0≤0.351.4
Missense OE?0.63 (0.54–0.74)
0≤0.61.4
Synonymous OE?0.98
0≤1.21.6
LoF obs/exp: 3 / 17.9Missense obs/exp: 105 / 166.7Syn Z: 0.14

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

CHTOP · 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