Is WNT9B p.Pro72Ser (c.214C>T) pathogenic?

WNT9B p.Pro72Ser (c.214C>T) is classified Uncertain significance in WNT9B (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-25). AlphaMissense: likely benign (0.2502); No allele count reported in gnomAD v4.1 (AN 1,613,624); Associated with Inborn genetic diseases.

What condition is associated with WNT9B p.Pro72Ser (c.214C>T)?

WNT9B p.Pro72Ser (c.214C>T) is associated with Inborn genetic diseases (ClinVar).

How common is WNT9B p.Pro72Ser (c.214C>T) in the general population?

WNT9B p.Pro72Ser (c.214C>T) is no allele count reported in gnomAD v4.1 (AN 1,613,624) (gnomAD).

What do computational predictors say about WNT9B p.Pro72Ser (c.214C>T)?

AlphaMissense predicts likely benign (score 0.2502) — an in-silico prediction, not a clinical call.

WNT9B p.Pro72Ser

c.214C>T · rs1282713416 · VCV3190765

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2502 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,624)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

⚠ 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
AlphaMissense	0.2502	likely benign
REVEL	0.684	pathogenic-leaning
SaProt	LLR -7.07	tolerated
⇒ REVEL calls this damaging; AlphaMissense and SaProt do not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 7.2	GERP 3.2, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 25 kb · p 0.05 · regional, not allelic
Overall
CADD	26.4	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,613,624). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: WNT9B
Protein: p.Pro72Ser
Coding: c.214C>T
MANE Select: NM_003396
dbSNP: rs1282713416
Type: single nucleotide variant
Location: chr17:46872653 (GRCh38)

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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-pro72ser (accessed [today's date]).

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