Is BAALC p.Ala40Ser (c.118G>T) pathogenic?

BAALC p.Ala40Ser (c.118G>T) is classified Uncertain significance in BAALC (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-15). AlphaMissense: likely benign (0.091); Absent from gnomAD v4.1.

How common is BAALC p.Ala40Ser (c.118G>T) in the general population?

BAALC p.Ala40Ser (c.118G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BAALC p.Ala40Ser (c.118G>T)?

AlphaMissense predicts likely benign (score 0.091) — an in-silico prediction, not a clinical call.

BAALC p.Ala40Ser

c.118G>T · VCV4191704

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.091 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,520,480)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.091	likely benign
REVEL	0.049	moderately benign-leaning
SaProt	LLR -6.97	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 6.4	GERP -0.057, phastCons 1
Regional constraint	o/e 1.04	unconstrained · MANE · 87 kb · p 0.53 · regional, not allelic
Overall
CADD	16.7	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 1,520,480). 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: BAALC
Protein: p.Ala40Ser
Coding: c.118G>T
MANE Select: NM_024812
Type: single nucleotide variant
Location: chr8:103141015 (GRCh38)
Gene constraint: LOEUF 1.439 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 60.47
Residue 40: the 'disordered' region

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

Similar variants

BAALC p.Ala35Val Uncertain significance ★ ⚠ same type
BAALC p.Ala41Gly Uncertain significance ★ ⚠ same type
BAALC p.Arg112Ser Uncertain significance ★ ⚠ same type
BAALC p.Arg137Gln Uncertain significance ★ ⚠ same type
BAALC p.Arg14Gly Uncertain significance ★ ⚠ same type
BAALC p.Arg21Gly Uncertain significance ★ ⚠ same type
BAALC p.Asp9Val Uncertain significance ★ ⚠ same type
BAALC p.Cys143Tyr 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/baalc-p-ala40ser (accessed [today's date]).

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