Is B4GALNT3 p.Ala239Val (c.716C>T) pathogenic?

B4GALNT3 p.Ala239Val (c.716C>T) is classified Uncertain significance in B4GALNT3 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-21). AlphaMissense: likely benign (0.1909); Absent from gnomAD v4.1.

How common is B4GALNT3 p.Ala239Val (c.716C>T) in the general population?

B4GALNT3 p.Ala239Val (c.716C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about B4GALNT3 p.Ala239Val (c.716C>T)?

AlphaMissense predicts likely benign (score 0.1909) — an in-silico prediction, not a clinical call.

B4GALNT3 p.Ala239Val

c.716C>T · rs2547232575 · VCV2338525

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1909 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,884)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1909	likely benign
REVEL	0.245	benign-leaning
SaProt	LLR -9.04	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.28	acceptor gain · deltas
Pangolin	Δ0.27	loss · gain 0.26 · SpliceAI calls gain · independent
Constraint at this position
Conservation	phyloP 5.8	GERP 2.1, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 17 kb · p 0.00032 · regional, not allelic
Overall
CADD	25.9	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 1,613,884). 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: B4GALNT3
Protein: p.Ala239Val
Coding: c.716C>T
MANE Select: NM_173593
dbSNP: rs2547232575
Type: single nucleotide variant
Location: chr12:548032 (GRCh38)
Gene constraint: LOEUF 0.835 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.56
Residue 239: the pa14 domain

Full B4GALNT3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

B4GALNT3 p.Arg686= Benign ★★ same type
B4GALNT3 p.Glu441Asp Benign ★★ same type
B4GALNT3 p.Gly752Val Benign ★★ same type
B4GALNT3 p.His536Tyr Benign ★★ same type
B4GALNT3 c.1271-1G>C Likely pathogenic ★ same type
B4GALNT3 p.Ala158Ser Uncertain significance ★ ⚠ same type
B4GALNT3 p.Ala28Val Uncertain significance ★ ⚠ same type
B4GALNT3 p.Ala319Thr 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/b4galnt3-p-ala239val (accessed [today's date]).

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