Is BUB1B p.Cys503= (c.1509T>C) pathogenic?

BUB1B p.Cys503= (c.1509T>C) is classified Likely benign in BUB1B (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-25). Ultra-rare (popmax 0.011%, sas); Associated with Inborn genetic diseases.

What condition is associated with BUB1B p.Cys503= (c.1509T>C)?

BUB1B p.Cys503= (c.1509T>C) is associated with Inborn genetic diseases (ClinVar).

How common is BUB1B p.Cys503= (c.1509T>C) in the general population?

BUB1B p.Cys503= (c.1509T>C) is ultra-rare (popmax 0.011%, sas) (gnomAD).

BUB1B p.Cys503=

c.1509T>C · rs544174035 · VCV3221351

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.011%, sas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.78	GERP 2, phastCons 0.79
Overall
CADD	5.751	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.011% South Asian · 10/91,018 alleles

Filtering AF 0.00594% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00453%

Overall 0.000682% 11/1,612,998 alleles · ultra-rare exomes 9/1,460,676 · genomes 2/152,322 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.011%	9,102
European (non-Finnish)	8.48e-05%	1,179,080

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: BUB1B
Protein: p.Cys503=
Coding: c.1509T>C
MANE Select: NM_001211
dbSNP: rs544174035
Type: single nucleotide variant
Location: chr15:40200351 (GRCh38)
Gene constraint: LOEUF 0.707 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 64.62 · 9 PDB

Full BUB1B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BUB1B p.Cys503Tyr Uncertain significance ★★ ⚠ same residue
BUB1B p.Cys503Phe Uncertain significance ★ ⚠ same residue
BUB1B c.35+4G>T Uncertain significance ★★ same condition
BUB1B p.Ala1017Thr Uncertain significance ★★ ⚠ same condition
BUB1B p.Ala1046Pro Uncertain significance ★★ ⚠ same condition
BUB1B p.Ala108Thr Uncertain significance ★★ ⚠ same condition
BUB1B p.Ala171Pro Uncertain significance ★★ ⚠ same condition
BUB1B p.Ala173Thr Uncertain significance ★★ ⚠ same condition

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/bub1b-p-cys503 (accessed [today's date]).

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