Is B9D2 p.Tyr171= (c.513C>T) pathogenic?

B9D2 p.Tyr171= (c.513C>T) is classified Benign/Likely benign in B9D2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-11-07). Rare (popmax 0.974%, eas); Associated with Joubert syndrome.

What condition is associated with B9D2 p.Tyr171= (c.513C>T)?

B9D2 p.Tyr171= (c.513C>T) is associated with Joubert syndrome, Meckel syndrome (ClinVar).

How common is B9D2 p.Tyr171= (c.513C>T) in the general population?

B9D2 p.Tyr171= (c.513C>T) is rare (popmax 0.974%, eas) (gnomAD).

B9D2 p.Tyr171=

c.513C>T · rs143680317 · VCV261882

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.974%, eas)

Conditions

Joubert 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 -3.7	GERP -2.6
Overall
CADD	0.11	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.974% East Asian · 437/44,886 alleles

Filtering AF 0.898% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.869%

Overall 0.0326% 526/1,614,022 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.974%	103
Remaining individualsnot grpmax-eligible	0.0208%	4,808
South Asian	0.0132%	7,591
African / African-American	0.00933%	10,720
Ashkenazi Jewishnot grpmax-eligible	0.00675%	14,804
European (non-Finnish)	0.00466%	21,455

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: B9D2
Protein: p.Tyr171=
Coding: c.513C>T
MANE Select: NM_030578
dbSNP: rs143680317
Type: single nucleotide variant
Location: chr19:41354715 (GRCh38)
Gene constraint: LOEUF 1.518 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.79

Full B9D2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Joubert syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Meckel syndrome

Similar variants

B9D2 p.Gly155Ser Pathogenic/Likely pathogenic ★★ same condition
B9D2 p.Pro74Ser Pathogenic/Likely pathogenic ★★ same condition
B9D2 p.Arg88Cys Uncertain significance ★★ ⚠ same condition
B9D2 p.Gln50His Uncertain significance ★★ ⚠ same condition
B9D2 p.Gly162Cys Uncertain significance ★★ ⚠ same condition
B9D2 p.Pro103Ser Uncertain significance ★★ ⚠ same condition
B9D2 p.Thr44Met Uncertain significance ★★ ⚠ same condition
B9D2 p.Val39Met 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/b9d2-p-tyr171 (accessed [today's date]).

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