Is BAD p.Arg116Ser (c.348G>C) pathogenic?

BAD p.Arg116Ser (c.348G>C) is classified Uncertain significance in BAD (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-08). AlphaMissense: likely pathogenic (0.951); Very rare (popmax 0.00503%, sas).

How common is BAD p.Arg116Ser (c.348G>C) in the general population?

BAD p.Arg116Ser (c.348G>C) is very rare (popmax 0.00503%, sas) (gnomAD).

What do computational predictors say about BAD p.Arg116Ser (c.348G>C)?

AlphaMissense predicts likely pathogenic (score 0.951) — an in-silico prediction, not a clinical call.

BAD p.Arg116Ser

c.348G>C · VCV3474444

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.951 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00503%, sas)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.951	likely pathogenic · top 4% in BAD
REVEL	0.61	indeterminate
SaProt	LLR -8.58	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.8	GERP 0.62, phastCons 1
Regional constraint	o/e 1.23	unconstrained · MANE · 14 kb · p 0.0004 · regional, not allelic
Overall
CADD	24.9	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

Grpmax group 0.00503% South Asian · 4/79,552 alleles

Filtering AF 0.00167% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000991%

Overall 0.000296% 4/1,351,668 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: BAD
Protein: p.Arg116Ser
Coding: c.348G>C
MANE Select: NM_032989
Type: single nucleotide variant
Location: chr11:64271643 (GRCh38)
Gene constraint: LOEUF 1.889 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.91 · 6 PDB
Residue 116: an α-helix

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

Similar variants

BAD p.Ala106Val Uncertain significance ★ ⚠ same type
BAD p.Ala138Thr Uncertain significance ★ ⚠ same type
BAD p.Ala41Thr 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-arg116ser (accessed [today's date]).

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