Is BUB1B p.Pro586= (c.1758C>T) pathogenic?

BUB1B p.Pro586= (c.1758C>T) is classified Likely benign in BUB1B (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-08). Very rare (popmax 6.2e-05%); Associated with Inborn genetic diseases.

What condition is associated with BUB1B p.Pro586= (c.1758C>T)?

BUB1B p.Pro586= (c.1758C>T) is associated with Inborn genetic diseases (ClinVar).

How common is BUB1B p.Pro586= (c.1758C>T) in the general population?

BUB1B p.Pro586= (c.1758C>T) is very rare (popmax 6.2e-05%) (gnomAD).

BUB1B p.Pro586=

c.1758C>T · rs2037634161 · VCV1779510

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 6.2e-05%)

Conditions

Inborn genetic diseases

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 -0.008	GERP -4.4, phastCons 0.059
Overall
CADD	5.913	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.2e-05%

Overall 6.2e-05% 1/1,614,082 alleles · very rare exomes 1/1,461,824 · genomes 0/152,258 · joint denominator

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.Pro586=
Coding: c.1758C>T
MANE Select: NM_001211
dbSNP: rs2037634161
Type: single nucleotide variant
Location: chr15:40206207 (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.Pro586Thr Uncertain significance ★ ⚠ same residue
BUB1B p.Pro586Ser Uncertain significance ★★ ⚠ same residue
BUB1B p.Pro586Arg 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

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-pro586 (accessed [today's date]).

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