Is BUB1B p.Lys438fs (c.1313_1317del) pathogenic?

BUB1B p.Lys438fs (c.13131317del) is classified Pathogenic in BUB1B (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-17). No gnomAD frequency available for this variant; Associated with mosaic variegated aneuploidy syndrome 1.

What condition is associated with BUB1B p.Lys438fs (c.1313_1317del)?

BUB1B p.Lys438fs (c.1313_1317del) is associated with mosaic variegated aneuploidy syndrome 1 (ClinVar).

How common is BUB1B p.Lys438fs (c.1313_1317del) in the general population?

BUB1B p.Lys438fs (c.1313_1317del) is no gnomAD frequency available for this variant (gnomAD).

BUB1B p.Lys438fs

c.1313_1317del · rs2542554796 · VCV2729407

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

mosaic variegated aneuploidy syndrome 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 10 of 23
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.1	GERP 0.96, phastCons 1
Region caveats
Repeat context	tandem	(AGAGCAG)n simple repeat · ambiguous alignment · confidence, not pathogenicity

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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.Lys438fs
Coding: c.1313_1317del
MANE Select: NM_001211
dbSNP: rs2542554796
Type: Microsatellite
Location: chr15:40199634 (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

mosaic variegated aneuploidy syndrome 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BUB1B p.Ser788fs Pathogenic/Likely pathogenic ★★ same condition
BUB1B p.Glu391del Uncertain significance ★★ same condition
BUB1B c.1568-15TC[2] Conflicting classifications of pathogenicity ★ same condition
BUB1B p.Glu215del Uncertain significance ★ same condition
BUB1B p.Lys540del Uncertain significance ★ same condition
BUB1B c.1058+8_1058+9del Likely benign ★ same condition
BUB1B c.1628+17_1628+24del Likely benign ★ same condition
BUB1B c.581+10_581+13del Likely benign ★ 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-lys438fs (accessed [today's date]).

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