Is CHERP p.Ala367Asp (c.1100C>A) pathogenic?

CHERP p.Ala367Asp (c.1100C>A) is classified Uncertain significance in CHERP (ClinVar, Single submitter, 1 submitter; last evaluated 2021-11-09). AlphaMissense: likely benign (0.2385); No allele count reported in gnomAD v4.1 (AN 1,558,144).

How common is CHERP p.Ala367Asp (c.1100C>A) in the general population?

CHERP p.Ala367Asp (c.1100C>A) is no allele count reported in gnomAD v4.1 (AN 1,558,144) (gnomAD).

What do computational predictors say about CHERP p.Ala367Asp (c.1100C>A)?

AlphaMissense predicts likely benign (score 0.2385) — an in-silico prediction, not a clinical call.

CHERP p.Ala367Asp

c.1100C>A · rs2513271358 · VCV2259867

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2385 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,558,144)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2385	likely benign
REVEL	0.045	moderately benign-leaning
SaProt	LLR -10.61	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.2	GERP 1.4, phastCons 1
Regional constraint	o/e 0.79	unconstrained · MANE · 9,052 bp · p 2.1e-07 · regional, not allelic
Overall
CADD	24.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,558,144). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CHERP
Protein: p.Ala367Asp
Coding: c.1100C>A
MANE Select: NM_006387
dbSNP: rs2513271358
Type: single nucleotide variant
Location: chr19:16529677 (GRCh38)
Gene constraint: LOEUF 0.152 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.55
Residue 367: the 'disordered' region

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.Ala403Gly Uncertain significance ★ ⚠ same type
CHERP p.Ala61Val Uncertain significance ★ ⚠ same type
CHERP p.Ala93Thr Uncertain significance ★ ⚠ same type
CHERP p.Ala94Val 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-ala367asp (accessed [today's date]).

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