Is CHERP p.Arg795Trp (c.2383C>T) pathogenic?

CHERP p.Arg795Trp (c.2383C>T) is classified Uncertain significance in CHERP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-12). AlphaMissense: likely benign (0.2484); Very rare (popmax 0.00439%, sas).

How common is CHERP p.Arg795Trp (c.2383C>T) in the general population?

CHERP p.Arg795Trp (c.2383C>T) is very rare (popmax 0.00439%, sas) (gnomAD).

What do computational predictors say about CHERP p.Arg795Trp (c.2383C>T)?

AlphaMissense predicts likely benign (score 0.2484) — an in-silico prediction, not a clinical call.

CHERP p.Arg795Trp

c.2383C>T · VCV4228027

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2484 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00439%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
AlphaMissense	0.2484	likely benign
REVEL	0.1	moderately benign-leaning
SaProt	LLR -9.40	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 1.2	GERP -2.3, phastCons 0.019
Regional constraint	o/e 0.86	unconstrained · MANE · 1,229 bp · p 0.049 · regional, not allelic
Overall
CADD	19.47	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00439% South Asian · 4/91,070 alleles

Filtering AF 0.00143% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000891%

Overall 0.00093% 15/1,613,508 alleles · very rare exomes 13/1,461,238 · genomes 2/152,270 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00439%	22,767
East Asian	0.00223%	44,872
Admixed American	0.00167%	60,020
European (non-Finnish)	0.000763%	131,115

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CHERP
Protein: p.Arg795Trp
Coding: c.2383C>T
MANE Select: NM_006387
Type: single nucleotide variant
Location: chr19:16520228 (GRCh38)

Full CHERP gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cherp-p-arg795trp (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown