Is WDR72 p.Val613= (c.1839G>A) pathogenic?

WDR72 p.Val613= (c.1839G>A) is classified Likely benign in WDR72 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2021-08-16). Common (popmax 7.38%, eas) — too common for a highly-penetrant pathogenic allele; Associated with amelogenesis imperfecta hypomaturation type 2A3.

What condition is associated with WDR72 p.Val613= (c.1839G>A)?

WDR72 p.Val613= (c.1839G>A) is associated with amelogenesis imperfecta hypomaturation type 2A3 (ClinVar).

WDR72 p.Val613=

Q: How common is WDR72 p.Val613= (c.1839G>A) in the general population?

WDR72 p.Val613= (c.1839G>A) is common (popmax 7.38%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1839G>A · rs78493456 · VCV316591

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 7.38%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

amelogenesis imperfecta hypomaturation type 2A3

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.12	GERP -0.69, phastCons 0.045
Overall
CADD	2.056	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 7.38% East Asian · 3,313/44,866 alleles

Filtering AF 7.17% ClinGen BA1/BS1 input FAF95, joint · FAF99 7.09%

Overall 1.68% 27,096/1,613,872 alleles · common exomes 25,111/1,461,606 · genomes 1,985/152,266 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	7.38%	14
South Asian	4.3%	23
Finnishnot grpmax-eligible	2.15%	47
Remaining individualsnot grpmax-eligible	1.75%	57
European (non-Finnish)	1.42%	71
Admixed American	0.712%	140
Middle Eastern	0.297%	336
African / African-American	0.289%	346
Ashkenazi Jewishnot grpmax-eligible	0.132%	759

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: WDR72
Protein: p.Val613=
Coding: c.1839G>A
MANE Select: NM_182758
dbSNP: rs78493456
Type: single nucleotide variant
Location: chr15:53665695 (GRCh38)
Gene constraint: LOEUF 1.089 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.22

Full WDR72 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

amelogenesis imperfecta hypomaturation type 2A3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

WDR72 p.Arg30Ter Pathogenic/Likely pathogenic ★★ same condition
WDR72 p.Arg896Ter Pathogenic/Likely pathogenic ★★ same condition
WDR72 p.Lys333Ter Pathogenic ★★ same condition
WDR72 p.Trp978Ter Pathogenic ★★ same condition
WDR72 c.*3852T>G Uncertain significance ★★ same condition
WDR72 p.Ala1094Thr Uncertain significance ★★ ⚠ same condition
WDR72 p.Ala373Val Uncertain significance ★★ ⚠ same condition
WDR72 p.Ala402Val 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/wdr72-p-val613 (accessed [today's date]).

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