Is CHERP p.Ile260= (c.780C>T) pathogenic?

CHERP p.Ile260= (c.780C>T) is classified Likely benign in CHERP (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-01). Very rare (popmax 0.00329%, sas).

How common is CHERP p.Ile260= (c.780C>T) in the general population?

CHERP p.Ile260= (c.780C>T) is very rare (popmax 0.00329%, sas) (gnomAD).

CHERP p.Ile260=

c.780C>T · rs369884233 · VCV2649513

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00329%, sas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -5.7	GERP -3.5
Overall
CADD	0.7	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00329% South Asian · 3/91,090 alleles

Filtering AF 0.000875% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000443%

Overall 0.000682% 11/1,613,850 alleles · very rare exomes 9/1,461,654 · genomes 2/152,196 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00329%	30,363
East Asian	0.00223%	44,874
Remaining individualsnot grpmax-eligible	0.0016%	62,482
African / African-American	0.00133%	74,938
European (non-Finnish)	0.000424%	236,002

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.Ile260=
Coding: c.780C>T
MANE Select: NM_006387
dbSNP: rs369884233
Type: single nucleotide variant
Location: chr19:16530775 (GRCh38)
Gene constraint: LOEUF 0.152 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.55
Residue 260: the cid domain

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

Similar variants

CHERP p.Ala125Glu Uncertain significance ★ ⚠ same type
CHERP p.Ala125Thr Uncertain significance ★ ⚠ same type
CHERP p.Ala125Val Uncertain significance ★ ⚠ same type
CHERP p.Ala175Val Uncertain significance ★ ⚠ same type
CHERP p.Ala367Asp Uncertain significance ★ ⚠ same type
CHERP p.Ala403Gly Uncertain significance ★ ⚠ same type
CHERP p.Ala61Val Uncertain significance ★ ⚠ same type
CHERP p.Ala93Thr Uncertain significance ★ ⚠ same type

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-ile260 (accessed [today's date]).

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