Is BID p.Arg118Trp (c.352C>T) pathogenic?

BID p.Arg118Trp (c.352C>T) is classified Uncertain significance in BID (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-16). AlphaMissense: likely benign (0.1257); Ultra-rare (popmax 0.0449%, eas).

How common is BID p.Arg118Trp (c.352C>T) in the general population?

BID p.Arg118Trp (c.352C>T) is ultra-rare (popmax 0.0449%, eas) (gnomAD).

What do computational predictors say about BID p.Arg118Trp (c.352C>T)?

AlphaMissense predicts likely benign (score 0.1257) — an in-silico prediction, not a clinical call.

BID p.Arg118Trp

c.352C>T · VCV4208810

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1257 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0449%, eas)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1257	likely benign
REVEL	0.118	moderately benign-leaning
SaProt	LLR -10.31	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.7	GERP 1.6, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 15 kb · p 0.061 · regional, not allelic
Overall
CADD	23.7	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

Grpmax group 0.0449% East Asian · 20/44,588 alleles

Filtering AF 0.0297% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0248%

Overall 0.00771% 123/1,595,986 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0449%	2,229
Admixed American	0.0236%	4,231
Middle Eastern	0.0167%	5,996
European (non-Finnish)	0.00724%	13,805
Remaining individualsnot grpmax-eligible	0.00323%	30,936
African / African-American	0.00134%	74,778

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: BID
Protein: p.Arg118Trp
Coding: c.352C>T
MANE Select: NM_001196
Type: single nucleotide variant
Location: chr22:17739360 (GRCh38)
Gene constraint: LOEUF 1.553 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.12 · 17 PDB
Residue 118: an α-helix

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

Similar variants

BID c.-14G>A Uncertain significance ★ same type
BID c.-15C>T Uncertain significance ★ same type
BID c.-23G>A Uncertain significance ★ same type
BID c.-24C>G Uncertain significance ★ same type
BID c.-33G>A Uncertain significance ★ same type
BID c.-39G>A Uncertain significance ★ same type
BID c.-59+698A>G Uncertain significance ★ same type
BID c.-59+722C>T 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/bid-p-arg118trp (accessed [today's date]).

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