Is BAD p.Ala100Thr (c.298G>A) pathogenic?

BAD p.Ala100Thr (c.298G>A) is classified Uncertain significance in BAD (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-26). AlphaMissense: likely pathogenic (0.7213); No allele count reported in gnomAD v4.1 (AN 1,472,534).

How common is BAD p.Ala100Thr (c.298G>A) in the general population?

BAD p.Ala100Thr (c.298G>A) is no allele count reported in gnomAD v4.1 (AN 1,472,534) (gnomAD).

What do computational predictors say about BAD p.Ala100Thr (c.298G>A)?

AlphaMissense predicts likely pathogenic (score 0.7213) — an in-silico prediction, not a clinical call.

BAD p.Ala100Thr

c.298G>A · VCV3984456

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7213 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,472,534)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.7213	likely pathogenic
REVEL	0.41	indeterminate
SaProt	LLR -7.68	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 7.6	GERP 1.8, phastCons 1
Regional constraint	o/e 1.23	unconstrained · MANE · 14 kb · p 0.0004 · regional, not allelic
Overall
CADD	28.7	PHRED · no single calibrated threshold — expert panels disagree

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 1,472,534). 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: BAD
Protein: p.Ala100Thr
Coding: c.298G>A
MANE Select: NM_001170880 · reported on NM_032989
Type: single nucleotide variant
Location: chr11:64271693 (GRCh38)

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

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/bad-p-ala100thr (accessed [today's date]).

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