Is BAHD1 p.Pro671Arg (c.2012C>G) pathogenic?

BAHD1 p.Pro671Arg (c.2012C>G) is classified Uncertain significance in BAHD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-26). AlphaMissense: likely pathogenic (0.9545); Absent from gnomAD v4.1.

How common is BAHD1 p.Pro671Arg (c.2012C>G) in the general population?

BAHD1 p.Pro671Arg (c.2012C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BAHD1 p.Pro671Arg (c.2012C>G)?

AlphaMissense predicts likely pathogenic (score 0.9545) — an in-silico prediction, not a clinical call.

BAHD1 p.Pro671Arg

c.2012C>G · VCV4192830

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9545 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9545	likely pathogenic
REVEL	0.857	moderately pathogenic-leaning
SaProt	LLR -12.13	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.9	GERP 1.6, phastCons 1
Regional constraint	o/e 0.46	unconstrained · MANE · 1,450 bp · p 7e-06 · regional, not allelic
Overall
CADD	29.7	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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: BAHD1
Protein: p.Pro671Arg
Coding: c.2012C>G
MANE Select: NM_014952
Type: single nucleotide variant
Location: chr15:40464507 (GRCh38)
Gene constraint: LOEUF 0.447 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 51.19
Residue 671: the bah domain

Full BAHD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BAHD1 p.Gln298Lys Benign ★★ same type
BAHD1 p.Ala200Thr Uncertain significance ★ ⚠ same type
BAHD1 p.Ala264Thr Uncertain significance ★ ⚠ same type
BAHD1 p.Ala409Thr Uncertain significance ★ ⚠ same type
BAHD1 p.Ala409Val Uncertain significance ★ ⚠ same type
BAHD1 p.Ala418Pro Uncertain significance ★ ⚠ same type
BAHD1 p.Ala462Ser Uncertain significance ★ ⚠ same type
BAHD1 p.Ala462Thr 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/bahd1-p-pro671arg (accessed [today's date]).

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