Is CTRB2 p.Asp196Asn (c.586G>A) pathogenic?

CTRB2 p.Asp196Asn (c.586G>A) is classified Uncertain significance in CTRB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-25). AlphaMissense: likely benign (0.1699); Very rare (popmax 0.00429%, amr).

How common is CTRB2 p.Asp196Asn (c.586G>A) in the general population?

CTRB2 p.Asp196Asn (c.586G>A) is very rare (popmax 0.00429%, amr) (gnomAD).

What do computational predictors say about CTRB2 p.Asp196Asn (c.586G>A)?

AlphaMissense predicts likely benign (score 0.1699) — an in-silico prediction, not a clinical call.

CTRB2 p.Asp196Asn

c.586G>A · VCV3837275

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1699 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00429%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1699	likely benign
REVEL	0.189	benign-leaning
SaProt	LLR -9.32	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -10	GERP -1.9
Regional constraint	o/e 0.64	unconstrained · MANE · 100 bp · p 0.018 · regional, not allelic
Overall
CADD	11.63	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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 0.00429% Admixed American · 2/46,674 alleles

Filtering AF 0.00071% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000266%

Overall 0.000427% 6/1,404,728 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00429%	23,337
East Asian	0.00253%	39,538
Remaining individualsnot grpmax-eligible	0.00182%	54,980
European (non-Finnish)	0.000194%	514,912

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.Asp196Asn
Coding: c.586G>A
MANE Select: NM_001025200
Type: single nucleotide variant
Location: chr16:75204817 (GRCh38)
Gene constraint: LOEUF 1.168 · pLI 0.36 (gnomAD)
Structure: AlphaFold pLDDT 91.79
Residue 196: 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.Ala244Thr Uncertain significance ★ ⚠ same type
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-asp196asn (accessed [today's date]).

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