Is WDR1 p.Pro244= (c.732C>T) pathogenic?

WDR1 p.Pro244= (c.732C>T) is classified Likely benign in WDR1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-12). Ultra-rare (popmax 0.058%, eas).

How common is WDR1 p.Pro244= (c.732C>T) in the general population?

WDR1 p.Pro244= (c.732C>T) is ultra-rare (popmax 0.058%, eas) (gnomAD).

WDR1 p.Pro244=

c.732C>T · rs202097102 · VCV1109878

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.058%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.52	acceptor gain · deltas
Constraint at this position
Conservation	phyloP -0.91	GERP -2.8
Overall
CADD	17.52	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.058% East Asian · 24/41,346 alleles

Filtering AF 0.04% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.034%

Overall 0.0148% 230/1,554,466 alleles · ultra-rare exomes 200/1,402,162 · genomes 30/152,304 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.0837%	1,194
East Asiangrpmax	0.058%	1,723
Admixed American	0.0175%	5,708
European (non-Finnish)	0.0138%	7,222
Remaining individualsnot grpmax-eligible	0.0133%	7,536
Finnishnot grpmax-eligible	0.005%	20,007
African / African-American	0.00409%	24,457

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: WDR1
Protein: p.Pro244=
Coding: c.732C>T
MANE Select: NM_017491
dbSNP: rs202097102
Type: single nucleotide variant
Location: chr4:10087926 (GRCh38)
Gene constraint: LOEUF 0.449 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 96.57 · 2 PDB

Full WDR1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

WDR1 p.Ala171Thr Uncertain significance ★★ ⚠ same type
WDR1 p.Ala360Ser Uncertain significance ★★ ⚠ same type
WDR1 p.Ala502Thr Uncertain significance ★★ ⚠ same type
WDR1 p.Arg158Gln Uncertain significance ★★ ⚠ same type
WDR1 p.Arg158Trp Uncertain significance ★★ ⚠ same type
WDR1 p.Arg161Gln Uncertain significance ★★ ⚠ same type
WDR1 p.Arg161Trp Uncertain significance ★★ ⚠ same type
WDR1 p.Arg470His Uncertain significance ★★ ⚠ same type

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/wdr1-p-pro244 (accessed [today's date]).

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