Is CHERP p.Ser763= (c.2289G>A) pathogenic?

CHERP p.Ser763= (c.2289G>A) is classified Likely benign in CHERP (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-01). Ultra-rare (popmax 0.0227%, afr).

How common is CHERP p.Ser763= (c.2289G>A) in the general population?

CHERP p.Ser763= (c.2289G>A) is ultra-rare (popmax 0.0227%, afr) (gnomAD).

CHERP p.Ser763=

c.2289G>A · rs376321664 · VCV2649511

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0227%, afr)

⚠ 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
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -2.8	GERP -3
Overall
CADD	6.013	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0227% African / African-American · 17/75,020 alleles

Filtering AF 0.0144% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0118%

Overall 0.00291% 47/1,614,072 alleles · ultra-rare exomes 30/1,461,858 · genomes 17/152,214 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0227%	4,413
Middle Eastern	0.0165%	6,062
East Asian	0.00669%	14,957
Admixed American	0.00667%	15,001
Remaining individualsnot grpmax-eligible	0.0064%	15,626
Finnishnot grpmax-eligible	0.00156%	63,992
European (non-Finnish)	0.00144%	69,413

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.Ser763=
Coding: c.2289G>A
MANE Select: NM_006387
dbSNP: rs376321664
Type: single nucleotide variant
Location: chr19:16520420 (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-ser763 (accessed [today's date]).

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