Is BUB3 p.Pro13= (c.39C>T) pathogenic?

BUB3 p.Pro13= (c.39C>T) is classified Likely benign in BUB3 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-16). Very rare (popmax 0.00333%, amr).

How common is BUB3 p.Pro13= (c.39C>T) in the general population?

BUB3 p.Pro13= (c.39C>T) is very rare (popmax 0.00333%, amr) (gnomAD).

BUB3 p.Pro13=

c.39C>T · rs773879591 · VCV1736860

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00333%, amr)

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 -1.8	GERP -2.7
Overall
CADD	12.65	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00333% Admixed American · 2/60,020 alleles

Filtering AF 0.000553% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000207%

Overall 0.000137% 2/1,461,818 alleles · very rare

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: BUB3
Protein: p.Pro13=
Coding: c.39C>T
MANE Select: NM_004725
dbSNP: rs773879591
Type: single nucleotide variant
Location: chr10:123154956 (GRCh38)
Gene constraint: LOEUF 0.77 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 96.10

Full BUB3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BUB3 p.Pro13Arg Uncertain significance ★ ⚠ same residue
BUB3 p.Pro13His Uncertain significance ★ ⚠ same residue
BUB3 p.Pro13Leu Uncertain significance ★ ⚠ same residue
BUB3 p.Pro13Ser Uncertain significance ★ ⚠ same residue
BUB3 p.Pro13Thr Uncertain significance ★ ⚠ same residue
BUB3 p.Arg314= Likely benign ★★ same type
BUB3 p.Ser197= Likely benign ★★ same type
BUB3 p.Ser198= Likely benign ★★ 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/bub3-p-pro13 (accessed [today's date]).

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