Is BBS4 p.Val402fs (c.1205_1208del) pathogenic?

BBS4 p.Val402fs (c.12051208del) is classified Likely pathogenic in BBS4 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-08-22). Very rare (popmax 0.0011%, sas); Associated with Bardet-Biedl syndrome 4.

What condition is associated with BBS4 p.Val402fs (c.1205_1208del)?

BBS4 p.Val402fs (c.1205_1208del) is associated with Bardet-Biedl syndrome 4 (ClinVar).

How common is BBS4 p.Val402fs (c.1205_1208del) in the general population?

BBS4 p.Val402fs (c.1205_1208del) is very rare (popmax 0.0011%, sas) (gnomAD).

How is Bardet-Biedl syndrome inherited?

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

BBS4 p.Val402fs

c.1205_1208del · rs767359099 · VCV2436750

Likely pathogenic Multiple submitters

Classification

Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Conditions

Bardet-Biedl syndrome 4

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 14 of 16
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.4	GERP 1.6, phastCons 1

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/91,074 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000248% 4/1,614,106 alleles · very rare exomes 4/1,461,862 · genomes 0/152,244 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0011%	91,074
European (non-Finnish)	0.000254%	393,334

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: BBS4
Protein: p.Val402fs
Coding: c.1205_1208del
MANE Select: NM_033028
dbSNP: rs767359099
Type: Deletion
Location: chr15:72735921 (GRCh38)
Gene constraint: LOEUF 0.953 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.36 · 1 PDB
Residue 402: the 'required for localization to centrosomes' region

Full BBS4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Bardet-Biedl syndrome 4 — 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

BBS4 c.1064_1106+97del Pathogenic/Likely pathogenic ★★ same condition
BBS4 p.Ala467fs Likely pathogenic ★★ same condition
BBS4 p.Leu114fs Pathogenic/Likely pathogenic ★★ same condition
BBS4 p.Leu310fs Pathogenic/Likely pathogenic ★★ same condition
BBS4 p.Leu381fs Pathogenic/Likely pathogenic ★★ same condition
BBS4 p.Lys358fs Pathogenic/Likely pathogenic ★★ same condition
BBS4 p.Pro30fs Pathogenic/Likely pathogenic ★★ same condition
BBS4 p.Ser409fs 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/bbs4-p-val402fs (accessed [today's date]).

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