Is BID p.Asp60Asn (c.178G>A) pathogenic?

BID p.Asp60Asn (c.178G>A) is classified Uncertain significance in BID (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-13). AlphaMissense: likely pathogenic (0.8485); Absent from gnomAD v4.1.

How common is BID p.Asp60Asn (c.178G>A) in the general population?

BID p.Asp60Asn (c.178G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BID p.Asp60Asn (c.178G>A)?

AlphaMissense predicts likely pathogenic (score 0.8485) — an in-silico prediction, not a clinical call.

BID p.Asp60Asn

c.178G>A · rs2518667040 · VCV2289577

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8485 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.8485	likely pathogenic · top 8% in BID
REVEL	0.363	indeterminate
SaProt	LLR -6.38	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 7.6	GERP 1.7, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 15 kb · p 0.061 · regional, not allelic
Overall
CADD	22.4	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: BID
Protein: p.Asp60Asn
Coding: c.178G>A
MANE Select: NM_001196
dbSNP: rs2518667040
Type: single nucleotide variant
Location: chr22:17743848 (GRCh38)
Gene constraint: LOEUF 1.553 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.12 · 17 PDB
Residue 60: a functional site (cleavage; by casp6)

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-asp60asn (accessed [today's date]).

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