Is CCER2 p.Glu232Ala (c.695A>C) pathogenic?

CCER2 p.Glu232Ala (c.695A>C) is classified Benign in CCER2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-06). AlphaMissense: likely benign (0.0787); Low-frequency (popmax 1.35%, eas).

How common is CCER2 p.Glu232Ala (c.695A>C) in the general population?

CCER2 p.Glu232Ala (c.695A>C) is low-frequency (popmax 1.35%, eas) (gnomAD).

What do computational predictors say about CCER2 p.Glu232Ala (c.695A>C)?

AlphaMissense predicts likely benign (score 0.0787) — an in-silico prediction, not a clinical call.

CCER2 p.Glu232Ala

c.695A>C · rs369436329 · VCV2859089

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0787 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.35%, eas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt

Computational evidence

Protein change
AlphaMissense	0.0787	likely benign
SaProt	LLR -7.72	tolerated
⇒ AlphaMissense and SaProt both call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · T>C here scores Δ0.24 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.63	GERP -1.4
Regional constraint	o/e 1.02	unconstrained · MANE · 2,919 bp · p 0.73 · regional, not allelic
Overall
CADD	6.516	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

Grpmax group 1.35% East Asian · 545/40,396 alleles

Filtering AF 1.26% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.22%

Overall 0.0854% 1,272/1,488,614 alleles · low-frequency

Ancestry group	Frequency	1 in
East Asiangrpmax	1.35%	74
South Asian	0.436%	230
Remaining individualsnot grpmax-eligible	0.16%	623
European (non-Finnish)	0.0246%	4,061
Middle Eastern	0.0174%	5,760
Admixed American	0.0155%	6,472
Finnishnot grpmax-eligible	0.0141%	7,115
African / African-American	0.00974%	10,271

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: CCER2
Protein: p.Glu232Ala
Coding: c.695A>C
MANE Select: NM_001243212
dbSNP: rs369436329
Type: single nucleotide variant
Location: chr19:38910579 (GRCh38)
Gene constraint: LOEUF 1.298 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.74
Residue 232: a UniProt-annotated variant site (in); the 'disordered' region

Full CCER2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCER2 p.Glu33Asp Benign ★★ ⚠ same type
CCER2 c.102+7A>T Uncertain significance ★ same type
CCER2 p.Ala121Gly Uncertain significance ★ ⚠ same type
CCER2 p.Ala21Ser Uncertain significance ★ ⚠ same type
CCER2 p.Arg123Leu Uncertain significance ★ ⚠ same type
CCER2 p.Arg143Lys Uncertain significance ★ ⚠ same type
CCER2 p.Arg195His Uncertain significance ★ ⚠ same type
CCER2 p.Glu202Lys 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/ccer2-p-glu232ala (accessed [today's date]).

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