Is GNB2 p.Ala35Val (c.104C>T) pathogenic?

GNB2 p.Ala35Val (c.104C>T) is classified Uncertain significance in GNB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-02). AlphaMissense: likely benign (0.1081); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with GNB2 p.Ala35Val (c.104C>T)?

GNB2 p.Ala35Val (c.104C>T) is associated with Inborn genetic diseases (ClinVar).

How common is GNB2 p.Ala35Val (c.104C>T) in the general population?

GNB2 p.Ala35Val (c.104C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about GNB2 p.Ala35Val (c.104C>T)?

AlphaMissense predicts likely benign (score 0.1081) — an in-silico prediction, not a clinical call.

GNB2 p.Ala35Val

c.104C>T · VCV3854503

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1081 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1081	likely benign
REVEL	0.132	moderately benign-leaning
SaProt	LLR -9.06	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 7.7	GERP 4.9, phastCons 1
Regional constraint	o/e 0.60	unconstrained · MANE · 2,532 bp · p 8.1e-18 · regional, not allelic
Overall
CADD	26.6	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: GNB2
Protein: p.Ala35Val
Coding: c.104C>T
MANE Select: NM_005273
Type: single nucleotide variant
Location: chr7:100676700 (GRCh38)
Gene constraint: LOEUF 0.372 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 96.89 · 1 PDB

Full GNB2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

GNB2 p.Thr198Lys Uncertain significance ★★ ⚠ same condition
GNB2 p.Arg129= Likely benign ★★ same condition
GNB2 p.Ala106Thr Uncertain significance ★ ⚠ same condition
GNB2 p.Ala309Thr Uncertain significance ★ ⚠ same condition
GNB2 p.Arg129Cys Uncertain significance ★ ⚠ same condition
GNB2 p.Arg129His Uncertain significance ★ ⚠ same condition
GNB2 p.Arg150Cys Uncertain significance ★ ⚠ same condition
GNB2 p.Arg49Lys Uncertain significance ★ ⚠ same condition

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/gnb2-p-ala35val (accessed [today's date]).

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