Is BRD10 p.Pro1679Ser (c.5035C>T) pathogenic?

BRD10 p.Pro1679Ser (c.5035C>T) is classified Uncertain significance in BRD10 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-08). AlphaMissense: likely benign (0.0935); Ultra-rare (popmax 0.0414%, afr).

How common is BRD10 p.Pro1679Ser (c.5035C>T) in the general population?

BRD10 p.Pro1679Ser (c.5035C>T) is ultra-rare (popmax 0.0414%, afr) (gnomAD).

What do computational predictors say about BRD10 p.Pro1679Ser (c.5035C>T)?

AlphaMissense predicts likely benign (score 0.0935) — an in-silico prediction, not a clinical call.

BRD10 p.Pro1679Ser

c.5035C>T · rs373083446 · VCV3235671

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0935 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0414%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0935	likely benign
REVEL	0.035	moderately benign-leaning
SaProt	LLR -5.20	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 3.7	GERP 0.81, phastCons 1
Regional constraint	o/e 1.35	unconstrained · MANE · 49 kb · p 2.6e-54 · regional, not allelic
Overall
CADD	14.54	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

Grpmax group 0.0414% African / African-American · 31/74,922 alleles

Filtering AF 0.0299% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.026%

Overall 0.0031% 50/1,613,828 alleles · ultra-rare exomes 25/1,461,622 · genomes 25/152,206 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0414%	2,417
Middle Eastern	0.0164%	6,084
Admixed American	0.0133%	7,500
Remaining individualsnot grpmax-eligible	0.0112%	8,923
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,604
East Asian	0.00223%	44,892
European (non-Finnish)	8.48e-05%	1,179,871

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: BRD10
Protein: p.Pro1679Ser
Coding: c.5035C>T
MANE Select: NM_001017969
dbSNP: rs373083446
Type: single nucleotide variant
Location: chr9:5920961 (GRCh38)
Structure: AlphaFold pLDDT 46.10

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

Similar variants

BRD10 p.Pro1679Leu Uncertain significance ★ ⚠ same residue
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

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-pro1679ser (accessed [today's date]).

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