Is BBS12 p.Cys470= (c.1410C>T) pathogenic?

BBS12 p.Cys470= (c.1410C>T) is classified Benign in BBS12 (ClinVar, Multiple submitters, 14 submitters; last evaluated 2026-05-18). Common (popmax 25.3%, nfe) — too common for a highly-penetrant pathogenic allele; Associated with Bardet-Biedl syndrome.

What condition is associated with BBS12 p.Cys470= (c.1410C>T)?

BBS12 p.Cys470= (c.1410C>T) is associated with Bardet-Biedl syndrome, Bardet-Biedl syndrome 1, Bardet-Biedl syndrome 12 (ClinVar).

How is Bardet-Biedl syndrome inherited?

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

BBS12 p.Cys470=

Q: How common is BBS12 p.Cys470= (c.1410C>T) in the general population?

BBS12 p.Cys470= (c.1410C>T) is common (popmax 25.3%, nfe) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1410C>T · rs13135445 · VCV166728

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 14 submitters

gnomAD v4.1

Common

common (popmax 25.3%, nfe) — too common for a highly-penetrant pathogenic allele

Conditions

Bardet-Biedl syndrome

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 -1.8	GERP -3.2
Overall
CADD	0.719	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 25.3% European (non-Finnish) · 298,256/1,179,872 alleles

Filtering AF 25.2% ClinGen BA1/BS1 input FAF95, joint · FAF99 25.2%

Overall 22.3% 360,139/1,613,942 alleles · common

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	25.3%	4
Finnishnot grpmax-eligible	20.9%	5
Remaining individualsnot grpmax-eligible	20.4%	5
Ashkenazi Jewishnot grpmax-eligible	19.5%	5
Middle Eastern	17.4%	6
Amishnot grpmax-eligible	16.7%	6
South Asian	13.8%	7
African / African-American	12.6%	8
Admixed American	11.3%	9
East Asian	0.0557%	1,796

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: BBS12
Protein: p.Cys470=
Coding: c.1410C>T
MANE Select: NM_152618
dbSNP: rs13135445
Type: single nucleotide variant
Location: chr4:122743302 (GRCh38)
Gene constraint: LOEUF 1.419 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.92

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

Also linked: Bardet-Biedl syndrome 1 Bardet-Biedl syndrome 12

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.Ala289Pro Likely pathogenic ★★ same condition
BBS12 p.Arg214Ter Pathogenic/Likely pathogenic ★★ same condition
BBS12 p.Arg355Ter Pathogenic ★★ same condition
BBS12 p.Arg675Ter Pathogenic/Likely pathogenic ★★ same condition
BBS12 p.Gln149Ter Pathogenic/Likely pathogenic ★★ same condition
BBS12 p.Gln228Ter Pathogenic/Likely pathogenic ★★ same condition
BBS12 p.Gln300Ter Pathogenic ★★ same condition
BBS12 p.Gln402Ter 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-cys470 (accessed [today's date]).

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