Is BUB1B p.Cys700= (c.2100T>C) pathogenic?

BUB1B p.Cys700= (c.2100T>C) is classified Likely benign in BUB1B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-02). No allele count reported in gnomAD v4.1 (AN 1,613,656); Associated with Inborn genetic diseases.

What condition is associated with BUB1B p.Cys700= (c.2100T>C)?

BUB1B p.Cys700= (c.2100T>C) is associated with Inborn genetic diseases (ClinVar).

How common is BUB1B p.Cys700= (c.2100T>C) in the general population?

BUB1B p.Cys700= (c.2100T>C) is no allele count reported in gnomAD v4.1 (AN 1,613,656) (gnomAD).

BUB1B p.Cys700=

c.2100T>C · rs1168839454 · VCV3221377

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,656)

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 0.87	GERP -2.7, phastCons 1
Overall
CADD	8.749	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,613,656). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BUB1B
Protein: p.Cys700=
Coding: c.2100T>C
MANE Select: NM_001211
dbSNP: rs1168839454
Type: single nucleotide variant
Location: chr15:40208727 (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.Cys700Tyr Uncertain significance ★★ ⚠ same residue
BUB1B p.Cys700Arg Uncertain significance ★ ⚠ same residue
BUB1B p.Cys700Ser 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-cys700 (accessed [today's date]).

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