WDR19 p.Pro375=
c.1125T>G · rs2109326804 · VCV1605169
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
Senior-Loken syndrome 8
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 -1.6 | GERP -3.1 |
| Overall | ||
| CADD | 6.843 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- WDR19
- Protein
- p.Pro375=
- Coding
- c.1125T>G
- MANE Select
- NM_025132
- dbSNP
- rs2109326804
- Type
- single nucleotide variant
- Location
- chr4:39216004 (GRCh38)
- Gene constraint
- LOEUF 0.833 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.44 · 4 PDB
- Residue 375
- a turn
Disease context
Senior-Loken syndrome 8 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: asphyxiating thoracic dystrophy 5
For Senior-Loken syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Adult, Childhood, Infancy
- Prevalence
- 1-9 / 1 000 000 (Worldwide)
Similar variants
- WDR19 p.Pro375fs Pathogenic/Likely pathogenic ★★ same residue
- WDR19 c.1135-2A>G Likely pathogenic ★★ same condition
- WDR19 c.1250-1G>A Pathogenic/Likely pathogenic ★★ same condition
- WDR19 c.1778-1G>A Likely pathogenic ★★ same condition
- WDR19 c.1982+2T>C Pathogenic/Likely pathogenic ★★ same condition
- WDR19 c.2363+1G>A Pathogenic/Likely pathogenic ★★ same condition
- WDR19 c.2364-2A>G Likely pathogenic ★★ same condition
- WDR19 c.2646-2A>G Likely pathogenic ★★ 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/wdr19-p-pro375 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown