Is ADGRB1 p.Val11Phe (c.31G>T) pathogenic?

ADGRB1 p.Val11Phe (c.31G>T) is classified Uncertain significance in ADGRB1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-02). AlphaMissense: likely benign (0.0714); Absent from gnomAD v4.1.

How common is ADGRB1 p.Val11Phe (c.31G>T) in the general population?

ADGRB1 p.Val11Phe (c.31G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ADGRB1 p.Val11Phe (c.31G>T)?

AlphaMissense predicts likely benign (score 0.0714) — an in-silico prediction, not a clinical call.

ADGRB1 p.Val11Phe

c.31G>T · VCV4238209

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0714 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,327,174)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0714	likely benign
REVEL	0.036	moderately benign-leaning
SaProt	LLR -7.79	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 -0.92	GERP -2.5
Regional constraint	o/e 1.00	unconstrained · MANE · 773 bp · p 1 · regional, not allelic
Overall
CADD	11.88	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

No allele count reported in gnomAD v4.1 (AN 1,327,174). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ADGRB1
Protein: p.Val11Phe
Coding: c.31G>T
MANE Select: NM_001702
Type: single nucleotide variant
Location: chr8:142464229 (GRCh38)
Gene constraint: LOEUF 0.372 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 62.83

Full ADGRB1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ADGRB1 p.Val11Gly Uncertain significance ★ ⚠ same residue
ADGRB1 c.2130+15C>G Benign ★★ same type
ADGRB1 p.Ala1507Val Benign ★★ same type
ADGRB1 p.Pro1295= Benign ★★ same type
ADGRB1 p.Pro575= Benign ★★ same type
ADGRB1 p.Ser480= Benign ★★ same type
ADGRB1 p.Thr1274= Benign ★★ same type
ADGRB1 p.Ala131Thr 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/adgrb1-p-val11phe (accessed [today's date]).

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