Is CCER2 p.Arg157Gln (c.470G>A) pathogenic?

CCER2 p.Arg157Gln (c.470G>A) is classified Likely benign in CCER2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-27). AlphaMissense: likely benign (0.0737); Rare (popmax 0.232%, afr).

How common is CCER2 p.Arg157Gln (c.470G>A) in the general population?

CCER2 p.Arg157Gln (c.470G>A) is rare (popmax 0.232%, afr) (gnomAD).

What do computational predictors say about CCER2 p.Arg157Gln (c.470G>A)?

AlphaMissense predicts likely benign (score 0.0737) — an in-silico prediction, not a clinical call.

CCER2 p.Arg157Gln

c.470G>A · VCV3671714

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0737 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.232%, afr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt

Computational evidence

Protein change
AlphaMissense	0.0737	likely benign
SaProt	LLR -6.99	tolerated
⇒ AlphaMissense and SaProt both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -7.1	GERP -4.2
Regional constraint	o/e 1.02	unconstrained · MANE · 2,919 bp · p 0.73 · regional, not allelic
Overall
CADD	0.002	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 0.232% African / African-American · 170/73,144 alleles

Filtering AF 0.204% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.193%

Overall 0.0217% 333/1,534,756 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.232%	430
South Asian	0.134%	749
Middle Eastern	0.0502%	1,993
Remaining individualsnot grpmax-eligible	0.0383%	2,612
Admixed American	0.0157%	6,364
East Asian	0.0122%	8,190
Finnishnot grpmax-eligible	0.00226%	44,242
European (non-Finnish)	0.00096%	104,197

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.Arg157Gln
Coding: c.470G>A
MANE Select: NM_001243212
Type: single nucleotide variant
Location: chr19:38910804 (GRCh38)
Gene constraint: LOEUF 1.298 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.74
Residue 157: 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-arg157gln (accessed [today's date]).

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