Is BBIP1 p.Lys3fs (c.6_7dup) pathogenic?

BBIP1 p.Lys3fs (c.67dup) is classified Uncertain significance in BBIP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-01-31). Absent from gnomAD.

How common is BBIP1 p.Lys3fs (c.6_7dup) in the general population?

BBIP1 p.Lys3fs (c.6_7dup) is absent from gnomAD (gnomAD).

BBIP1 p.Lys3fs

c.6_7dup · rs2134053273 · VCV1053366

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 2 of 4
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.5	GERP 0.66, phastCons 0.98

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: BBIP1
Protein: p.Lys3fs
Coding: c.6_7dup
MANE Select: NM_001195305
dbSNP: rs2134053273
Type: Duplication
Location: chr10:110918150 (GRCh38)
Gene constraint: LOEUF 1.693 · pLI 0.07 (gnomAD)
Structure: AlphaFold pLDDT 82.24 · 1 PDB
Residue 3: the 'disordered' region

Full BBIP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BBIP1 p.Glu84fs Uncertain significance ★★ same type
BBIP1 p.Leu50dup Uncertain significance ★★ same type
BBIP1 p.Arg31fs Uncertain significance ★ same type
BBIP1 p.Asn15fs Uncertain significance ★ same type
BBIP1 p.Met69fs Uncertain significance ★ same type
BBIP1 p.Ser60fs Uncertain significance ★ same type
BBIP1 c.37+3dup 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/bbip1-p-lys3fs (accessed [today's date]).

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