Is BAD p.Ala106Val (c.317C>T) pathogenic?

BAD p.Ala106Val (c.317C>T) is classified Uncertain significance in BAD (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-26). AlphaMissense: ambiguous (0.3829); Absent from gnomAD v4.1.

How common is BAD p.Ala106Val (c.317C>T) in the general population?

BAD p.Ala106Val (c.317C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BAD p.Ala106Val (c.317C>T)?

AlphaMissense predicts ambiguous (score 0.3829) — an in-silico prediction, not a clinical call.

BAD p.Ala106Val

c.317C>T · VCV4645060

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3829 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,501,034)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.3829	ambiguous
REVEL	0.257	benign-leaning
SaProt	LLR -7.12	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.4	GERP 1.8, phastCons 1
Regional constraint	o/e 1.23	unconstrained · MANE · 14 kb · p 0.0004 · regional, not allelic
Overall
CADD	28.9	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 1,501,034). 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.Ala106Val
Coding: c.317C>T
MANE Select: NM_032989
Type: single nucleotide variant
Location: chr11:64271674 (GRCh38)
Gene constraint: LOEUF 1.889 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.91 · 6 PDB

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

Similar variants

BAD p.Ala138Thr Uncertain significance ★ ⚠ same type
BAD p.Ala41Thr Uncertain significance ★ ⚠ same type
BAD p.Arg116Ser Uncertain significance ★ ⚠ same type
BAD p.Arg161Gly Uncertain significance ★ ⚠ same type
BAD p.Asp82Asn Uncertain significance ★ ⚠ same type
BAD p.Gln152Arg Uncertain significance ★ ⚠ same type
BAD p.Glu81Gln Uncertain significance ★ ⚠ same type
BAD p.Gly160Arg 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/bad-p-ala106val (accessed [today's date]).

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