Is BRD10 p.Pro417Arg (c.1250C>G) pathogenic?

BRD10 p.Pro417Arg (c.1250C>G) is classified Uncertain significance in BRD10 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-21). AlphaMissense: likely benign (0.1281); Absent from gnomAD v4.1.

How common is BRD10 p.Pro417Arg (c.1250C>G) in the general population?

BRD10 p.Pro417Arg (c.1250C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BRD10 p.Pro417Arg (c.1250C>G)?

AlphaMissense predicts likely benign (score 0.1281) — an in-silico prediction, not a clinical call.

BRD10 p.Pro417Arg

c.1250C>G · rs976179771 · VCV3235628

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1281 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1281	likely benign
REVEL	0.159	moderately benign-leaning
SaProt	LLR -4.97	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.8	GERP 2.2, phastCons 1
Regional constraint	o/e 1.20	unconstrained · MANE · 39 kb · p 3.1e-06 · regional, not allelic
Overall
CADD	22.2	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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: BRD10
Protein: p.Pro417Arg
Coding: c.1250C>G
MANE Select: NM_001017969
dbSNP: rs976179771
Type: single nucleotide variant
Location: chr9:5968981 (GRCh38)
Structure: AlphaFold pLDDT 46.10

Full BRD10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BRD10 p.Pro1552= Benign ★★ same type
BRD10 p.Val1306Leu Likely benign ★★ same type
BRD10 p.Ala1032Pro Uncertain significance ★ ⚠ same type
BRD10 p.Ala1150Thr Uncertain significance ★ ⚠ same type
BRD10 p.Ala116Val Uncertain significance ★ ⚠ same type
BRD10 p.Ala1182Gly Uncertain significance ★ ⚠ same type
BRD10 p.Ala1225Gly Uncertain significance ★ ⚠ same type
BRD10 p.Ala1256Val 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/brd10-p-pro417arg (accessed [today's date]).

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