Is WNT9B p.Ala321= (c.963G>A) pathogenic?

WNT9B p.Ala321= (c.963G>A) is classified Likely benign in WNT9B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-28). Rare (popmax 0.581%, afr); Associated with WNT9B-related disorder.

What condition is associated with WNT9B p.Ala321= (c.963G>A)?

WNT9B p.Ala321= (c.963G>A) is associated with WNT9B-related disorder (ClinVar).

How common is WNT9B p.Ala321= (c.963G>A) in the general population?

WNT9B p.Ala321= (c.963G>A) is rare (popmax 0.581%, afr) (gnomAD).

WNT9B p.Ala321=

c.963G>A · rs145757598 · VCV3040481

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.581%, afr)

Conditions

WNT9B-related disorder

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -3.3	GERP -1.3
Overall
CADD	0.309	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.581% African / African-American · 285/49,060 alleles

Filtering AF 0.525% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.504%

Overall 0.0868% 379/436,620 alleles · rare exomes 110/284,528 · genomes 269/152,092 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.581%	172
East Asian	0.179%	559
Remaining individualsnot grpmax-eligible	0.0778%	1,285
Admixed American	0.0596%	1,678
South Asian	0.0288%	3,467
European (non-Finnish)	0.00742%	13,473

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: WNT9B
Protein: p.Ala321=
Coding: c.963G>A
MANE Select: NM_003396 · reported on NM_001320458
dbSNP: rs145757598
Type: single nucleotide variant
Location: chr17:46885092 (GRCh38)

Full WNT9B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

WNT9B-related disorder

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/wnt9b-p-ala321 (accessed [today's date]).

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