Is BBS2 p.Gln693= (c.2079G>A) pathogenic?

BBS2 p.Gln693= (c.2079G>A) is classified Benign/Likely benign in BBS2 (ClinVar, Multiple submitters, 8 submitters; last evaluated 2026-01-28). Low-frequency (popmax 2.58%, eas); Associated with Bardet-Biedl syndrome 2.

What condition is associated with BBS2 p.Gln693= (c.2079G>A)?

BBS2 p.Gln693= (c.2079G>A) is associated with Bardet-Biedl syndrome 2, Bardet-Biedl syndrome, inherited retinal dystrophy (ClinVar).

How common is BBS2 p.Gln693= (c.2079G>A) in the general population?

BBS2 p.Gln693= (c.2079G>A) is low-frequency (popmax 2.58%, eas) (gnomAD).

How is Bardet-Biedl syndrome inherited?

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

BBS2 p.Gln693=

c.2079G>A · rs150797250 · VCV319849

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

gnomAD v4.1

Rare

low-frequency (popmax 2.58%, eas)

Conditions

Bardet-Biedl syndrome 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.11	GERP -3.5, phastCons 0.58
Overall
CADD	4.096	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.58% East Asian · 1,158/44,858 alleles

Filtering AF 2.46% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.41%

Overall 0.0863% 1,393/1,613,970 alleles · low-frequency

Ancestry group	Frequency	1 in
East Asiangrpmax	2.58%	39
South Asian	0.0867%	1,153
Ashkenazi Jewishnot grpmax-eligible	0.0811%	1,233
Remaining individualsnot grpmax-eligible	0.0784%	1,275
Middle Eastern	0.0165%	6,062
European (non-Finnish)	0.00636%	15,732
Finnishnot grpmax-eligible	0.00625%	16,002
Admixed American	0.005%	20,005

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: BBS2
Protein: p.Gln693=
Coding: c.2079G>A
MANE Select: NM_031885
dbSNP: rs150797250
Type: single nucleotide variant
Location: chr16:56484848 (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

Bardet-Biedl syndrome 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Bardet-Biedl syndrome inherited retinal dystrophy

For Bardet-Biedl syndrome (Orphanet):

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

Similar variants

BBS2 p.Gln693fs Likely pathogenic ★ same residue
BBS2 c.118-1G>T Likely pathogenic ★★ same condition
BBS2 c.118-2A>C Likely pathogenic ★★ same condition
BBS2 c.118-2A>G Likely pathogenic ★★ same condition
BBS2 c.1225+2T>C Likely pathogenic ★★ same condition
BBS2 c.1225+2T>G Likely pathogenic ★★ same condition
BBS2 c.1397+1G>A Pathogenic/Likely pathogenic ★★ same condition
BBS2 c.1397+2T>C 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/bbs2-p-gln693 (accessed [today's date]).

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