Is CCER2 p.Thr68Ser (c.202A>T) pathogenic?

CCER2 p.Thr68Ser (c.202A>T) is classified Benign in CCER2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-24). AlphaMissense: likely benign (0.1721); Low-frequency (popmax 1.2%, nfe).

How common is CCER2 p.Thr68Ser (c.202A>T) in the general population?

CCER2 p.Thr68Ser (c.202A>T) is low-frequency (popmax 1.2%, nfe) (gnomAD).

What do computational predictors say about CCER2 p.Thr68Ser (c.202A>T)?

AlphaMissense predicts likely benign (score 0.1721) — an in-silico prediction, not a clinical call.

CCER2 p.Thr68Ser

c.202A>T · rs117592327 · VCV2045526

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1721 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.2%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, SaProt

Computational evidence

Protein change
AlphaMissense	0.1721	likely benign
SaProt	LLR -5.36	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 -0.46	GERP -2.7
Regional constraint	o/e 1.02	unconstrained · MANE · 2,919 bp · p 0.73 · regional, not allelic
Overall
CADD	2.445	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 1.2% European (non-Finnish) · 13,142/1,098,598 alleles

Filtering AF 1.18% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.17%

Overall 1.02% 14,548/1,433,288 alleles · low-frequency

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	1.2%	84
Ashkenazi Jewishnot grpmax-eligible	1.15%	87
Finnishnot grpmax-eligible	0.952%	105
Remaining individualsnot grpmax-eligible	0.691%	145
Admixed American	0.598%	167
Amishnot grpmax-eligible	0.439%	228
African / African-American	0.205%	489
Middle Eastern	0.0546%	1,832
South Asian	0.0352%	2,838

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.Thr68Ser
Coding: c.202A>T
MANE Select: NM_001243212
dbSNP: rs117592327
Type: single nucleotide variant
Location: chr19:38911072 (GRCh38)
Gene constraint: LOEUF 1.298 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.74

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-thr68ser (accessed [today's date]).

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