Is BBS2 p.Phe6fs (c.15_16del) pathogenic?

BBS2 p.Phe6fs (c.1516del) is classified Likely pathogenic in BBS2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-05-24). Associated with BBS2-related disorder.

What condition is associated with BBS2 p.Phe6fs (c.15_16del)?

BBS2 p.Phe6fs (c.15_16del) is associated with BBS2-related disorder (ClinVar).

BBS2 p.Phe6fs

c.15_16del · VCV4930080

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

BBS2-related disorder

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 1 of 17
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2, phastCons 1

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

Variant & gene context

Gene: BBS2
Protein: p.Phe6fs
Coding: c.15_16del
MANE Select: NM_031885
Type: Microsatellite
Location: chr16:56519847 (GRCh38)
Gene constraint: LOEUF 0.892 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.49

Full BBS2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

BBS2-related disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BBS2 c.804+1_804+14del Likely pathogenic ★★ same condition
BBS2 c.941-1G>T Pathogenic/Likely pathogenic ★★ same condition
BBS2 p.Arg216Pro Likely pathogenic ★★ same condition
BBS2 p.Arg234Ter Pathogenic ★★ same condition
BBS2 p.Arg275Ter Pathogenic/Likely pathogenic ★★ same condition
BBS2 p.Arg703Ter Pathogenic/Likely pathogenic ★★ same condition
BBS2 p.Asn663Ter Pathogenic/Likely pathogenic ★★ same condition
BBS2 p.Asp104Ala Pathogenic ★★ 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/bbs2-p-phe6fs (accessed [today's date]).

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