Is BBS7 p.Cys152Phe (c.455G>T) pathogenic?

BBS7 p.Cys152Phe (c.455G>T) is classified Uncertain significance in BBS7 (ClinVar, Single submitter, 1 submitter). AlphaMissense: ambiguous (0.5085); Very rare (popmax 8.48e-05%, nfe); Associated with Bardet-Biedl syndrome 7.

What condition is associated with BBS7 p.Cys152Phe (c.455G>T)?

BBS7 p.Cys152Phe (c.455G>T) is associated with Bardet-Biedl syndrome 7 (ClinVar).

How common is BBS7 p.Cys152Phe (c.455G>T) in the general population?

BBS7 p.Cys152Phe (c.455G>T) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

How is Bardet-Biedl syndrome inherited?

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

What do computational predictors say about BBS7 p.Cys152Phe (c.455G>T)?

AlphaMissense predicts ambiguous (score 0.5085) — an in-silico prediction, not a clinical call.

BBS7 p.Cys152Phe

c.455G>T · rs2476548413 · VCV3242540

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5085 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

Conditions

Bardet-Biedl syndrome 7

Computational evidence

Protein change
AlphaMissense	0.5085	ambiguous
REVEL	0.59	indeterminate
SaProt	LLR -12.48	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.5, phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 44 kb · p 0.00015 · regional, not allelic
Overall
CADD	27.2	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.48e-05% European (non-Finnish) · 1/1,179,866 alleles

Overall 6.84e-05% 1/1,461,674 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: BBS7
Protein: p.Cys152Phe
Coding: c.455G>T
MANE Select: NM_176824
dbSNP: rs2476548413
Type: single nucleotide variant
Location: chr4:121859065 (GRCh38)
Gene constraint: LOEUF 0.701 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 92.99

Full BBS7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Bardet-Biedl syndrome 7 — 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

BBS7 p.Cys152Arg Uncertain significance ★ ⚠ same residue
BBS7 p.Cys152Ser Uncertain significance ★ ⚠ same residue
BBS7 c.1371+1G>A Likely pathogenic ★★ same condition
BBS7 c.1512-1G>A Likely pathogenic ★★ same condition
BBS7 c.1677-2A>G Pathogenic/Likely pathogenic ★★ same condition
BBS7 c.1891-2A>C Pathogenic/Likely pathogenic ★★ same condition
BBS7 c.529-2A>G Pathogenic/Likely pathogenic ★★ same condition
BBS7 c.849+1G>C Pathogenic/Likely 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/bbs7-p-cys152phe (accessed [today's date]).

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