CHTOP

Chr 1

chromatin target of PRMT1

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

NCBI Gene: 26097 ENSG00000160679 UniProt: Q9Y3Y2 OMIM: 614206

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]

OMIM Research

OMIM ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.43

Clinical Summary— CHTOP

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Population Constraint (gnomAD)

Moderately constrained gene (pLI 0.76) — some intolerance to loss-of-function variants.

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ClinVar Variants

33 VUS of 48 total submissions

Explore recent and relevant literature in Research Assistant →

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

This gene — mechanism propensity

0.5181th %ile

GOF

0.3094th %ile

LOF

0.72top 10%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.43

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

48 submitted variants in ClinVar

ClinVar

Classification Summary

VUS33

Likely Benign3

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	33	0	33
Likely Benign	2	1	3
Benign	0	0	0
Total	35	1	36

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

9 pathogenic / likely-pathogenic (of 19) ClinVar copy-number / structural variants overlap CHTOP — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →