Is BBS9 p.Ser635fs (c.1903del) pathogenic?

BBS9 p.Ser635fs (c.1903del) is classified Likely pathogenic in BBS9 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-08). Absent from gnomAD; Associated with Bardet-Biedl syndrome 9.

What condition is associated with BBS9 p.Ser635fs (c.1903del)?

BBS9 p.Ser635fs (c.1903del) is associated with Bardet-Biedl syndrome 9 (ClinVar).

How common is BBS9 p.Ser635fs (c.1903del) in the general population?

BBS9 p.Ser635fs (c.1903del) 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.

BBS9 p.Ser635fs

c.1903del · rs2536327971 · VCV3240906

Likely pathogenic Single submitter

Classification

Likely 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 9

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 18 of 23
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.9	GERP 1.6, phastCons 1

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: BBS9
Protein: p.Ser635fs
Coding: c.1903del
MANE Select: NM_198428
dbSNP: rs2536327971
Type: Deletion
Location: chr7:33383778 (GRCh38)
Gene constraint: LOEUF 0.959 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.41 · 2 PDB

Full BBS9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Bardet-Biedl syndrome 9 — 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

BBS9 p.Cys104fs Pathogenic/Likely pathogenic ★★ same condition
BBS9 p.Glu604fs Pathogenic/Likely pathogenic ★★ same condition
BBS9 p.Gly145fs Pathogenic ★★ same condition
BBS9 p.Gly43fs Likely pathogenic ★★ same condition
BBS9 p.Ile392fs Pathogenic/Likely pathogenic ★★ same condition
BBS9 p.Lys626fs Pathogenic ★★ same condition
BBS9 p.Val72fs Pathogenic/Likely pathogenic ★★ same condition
BBS9 p.Glu765_Leu766delinsVal Uncertain significance ★★ 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/bbs9-p-ser635fs (accessed [today's date]).

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