Is CTRB2 p.Gly202Arg (c.604G>A) pathogenic?

CTRB2 p.Gly202Arg (c.604G>A) is classified Uncertain significance in CTRB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-23). AlphaMissense: likely pathogenic (0.8374); Very rare (popmax 0.00376%, sas).

How common is CTRB2 p.Gly202Arg (c.604G>A) in the general population?

CTRB2 p.Gly202Arg (c.604G>A) is very rare (popmax 0.00376%, sas) (gnomAD).

What do computational predictors say about CTRB2 p.Gly202Arg (c.604G>A)?

AlphaMissense predicts likely pathogenic (score 0.8374) — an in-silico prediction, not a clinical call.

CTRB2 p.Gly202Arg

c.604G>A · rs1378576714 · VCV2520874

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8374 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00376%, sas)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8374	likely pathogenic
REVEL	0.849	moderately pathogenic-leaning
SaProt	LLR -17.13	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.7	GERP 2, phastCons 0.87
Regional constraint	o/e 1.32	unconstrained · MANE · 639 bp · p 0.0022 · regional, not allelic
Overall
CADD	23.2	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00376% South Asian · 3/79,716 alleles

Filtering AF 0.000999% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000477%

Overall 0.00104% 15/1,438,926 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00376%	26,572
East Asian	0.00251%	39,870
Finnishnot grpmax-eligible	0.00179%	55,898
Remaining individualsnot grpmax-eligible	0.00179%	55,902
European (non-Finnish)	0.000849%	117,773

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: CTRB2
Protein: p.Gly202Arg
Coding: c.604G>A
MANE Select: NM_001025200
dbSNP: rs1378576714
Type: single nucleotide variant
Location: chr16:75204799 (GRCh38)
Gene constraint: LOEUF 1.168 · pLI 0.36 (gnomAD)
Structure: AlphaFold pLDDT 91.79
Residue 202: a disulfide bond; the peptidase s1 domain

Full CTRB2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

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CTRB2 p.Arg131His Uncertain significance ★ ⚠ same type
CTRB2 p.Arg236Cys Uncertain significance ★ ⚠ same type
CTRB2 p.Arg236His Uncertain significance ★ ⚠ same type
CTRB2 p.Arg248Cys Uncertain significance ★ ⚠ same type
CTRB2 p.Asn167Tyr 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/ctrb2-p-gly202arg (accessed [today's date]).

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