Is BRAP p.Thr355= (c.1065G>A) pathogenic?

BRAP p.Thr355= (c.1065G>A) is classified Benign in BRAP (ClinVar, Single submitter, 1 submitter; last evaluated 2017-12-13). Rare (popmax 0.342%, nfe).

How common is BRAP p.Thr355= (c.1065G>A) in the general population?

BRAP p.Thr355= (c.1065G>A) is rare (popmax 0.342%, nfe) (gnomAD).

BRAP p.Thr355=

c.1065G>A · rs151101195 · VCV781699

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.342%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -20	GERP -3.1
Overall
CADD	0.399	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.342% European (non-Finnish) · 4,041/1,180,008 alleles

Filtering AF 0.334% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.33%

Overall 0.298% 4,818/1,614,114 alleles · rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.512%	195
European (non-Finnish)grpmax	0.342%	292
Remaining individualsnot grpmax-eligible	0.339%	295
Admixed American	0.13%	769
South Asian	0.102%	979
Middle Eastern	0.099%	1,010
Ashkenazi Jewishnot grpmax-eligible	0.0709%	1,410
African / African-American	0.0426%	2,346
East Asian	0.0156%	6,411

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: BRAP
Protein: p.Thr355=
Coding: c.1065G>A
MANE Select: NM_006768
dbSNP: rs151101195
Type: single nucleotide variant
Location: chr12:111659253 (GRCh38)
Gene constraint: LOEUF 0.766 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.92

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

Similar variants

BRAP p.Ala42= Benign ★★ same type
BRAP p.Gly250= Benign ★★ same type
BRAP p.Ile193= Benign ★★ same type
BRAP p.Lys451= Benign ★★ same type
BRAP p.Ala100Val Uncertain significance ★ ⚠ same type
BRAP p.Ala379Val Uncertain significance ★ same type
BRAP p.Ala403Ser Uncertain significance ★ ⚠ same type
BRAP p.Ala481Gly 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/brap-p-thr355 (accessed [today's date]).

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