Is BBS12 p.Pro159fs (c.476del) pathogenic?

BBS12 p.Pro159fs (c.476del) is classified Pathogenic in BBS12 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-17). Absent from gnomAD; Associated with Bardet-Biedl syndrome.

What condition is associated with BBS12 p.Pro159fs (c.476del)?

BBS12 p.Pro159fs (c.476del) is associated with Bardet-Biedl syndrome (ClinVar).

How common is BBS12 p.Pro159fs (c.476del) in the general population?

BBS12 p.Pro159fs (c.476del) is absent from gnomAD (gnomAD).

How is Bardet-Biedl syndrome inherited?

Typically Autosomal recessive, Oligogenic (Orphanet). A genetic counselor can assess individual risk for a family.

BBS12 p.Pro159fs

c.476del · rs777861896 · VCV2821668

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

Bardet-Biedl syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (2 of 2) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.82	GERP -3.5

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: BBS12
Protein: p.Pro159fs
Coding: c.476del
MANE Select: NM_152618
dbSNP: rs777861896
Type: Deletion
Location: chr4:122742367 (GRCh38)
Gene constraint: LOEUF 1.419 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.92
Residue 159: a UniProt-annotated variant site (in bbs12; uncertain significance; significantly reduces the interaction with mkks; the interaction with bbs10 is not affected by this mutation)

Full BBS12 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Bardet-Biedl syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Bardet-Biedl syndrome (Orphanet):

Inheritance: Autosomal recessive, Oligogenic
Onset: Antenatal, Childhood, Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Specific population)

Similar variants

BBS12 p.Pro159Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
BBS12 p.Asn485fs Pathogenic/Likely pathogenic ★★ same condition
BBS12 p.Asn649_Ser650insTer Pathogenic/Likely pathogenic ★★ same condition
BBS12 p.Asp383fs Pathogenic/Likely pathogenic ★★ same condition
BBS12 p.Cys140fs Pathogenic ★★ same condition
BBS12 p.Cys304fs Pathogenic/Likely pathogenic ★★ same condition
BBS12 p.Gln511_Gln513del Pathogenic/Likely pathogenic ★★ same condition
BBS12 p.Glu365fs 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/bbs12-p-pro159fs (accessed [today's date]).

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