Is WDR19 p.Ser25= (c.75A>G) pathogenic?

WDR19 p.Ser25= (c.75A>G) is classified Likely benign in WDR19 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-08-28). No allele count reported in gnomAD v4.1 (AN 1,556,074); Associated with Senior-Loken syndrome 8.

What condition is associated with WDR19 p.Ser25= (c.75A>G)?

WDR19 p.Ser25= (c.75A>G) is associated with Senior-Loken syndrome 8, asphyxiating thoracic dystrophy 5 (ClinVar).

How common is WDR19 p.Ser25= (c.75A>G) in the general population?

WDR19 p.Ser25= (c.75A>G) is no allele count reported in gnomAD v4.1 (AN 1,556,074) (gnomAD).

How is Senior-Loken syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

WDR19 p.Ser25=

c.75A>G · rs1389886639 · VCV1113043

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,556,074)

Conditions

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 0.77	GERP -1.1, phastCons 0.98
Overall
CADD	6.845	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,556,074). 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: WDR19
Protein: p.Ser25=
Coding: c.75A>G
MANE Select: NM_025132
dbSNP: rs1389886639
Type: single nucleotide variant
Location: chr4:39185794 (GRCh38)
Gene constraint: LOEUF 0.833 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.44 · 4 PDB
Residue 25: a turn

Full WDR19 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Senior-Loken syndrome 8 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also 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.Ser25Pro Uncertain significance ★ ⚠ 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-ser25 (accessed [today's date]).

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