Is DOLK p.Val232del (c.684GGT[2]) pathogenic?

DOLK p.Val232del (c.684GGT[2]) is classified Uncertain significance in DOLK (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-19). Very rare (popmax 0.000254%, nfe); Associated with DK1-congenital disorder of glycosylation.

What condition is associated with DOLK p.Val232del (c.684GGT[2])?

DOLK p.Val232del (c.684GGT[2]) is associated with DK1-congenital disorder of glycosylation (ClinVar).

How common is DOLK p.Val232del (c.684GGT[2]) in the general population?

DOLK p.Val232del (c.684GGT[2]) is very rare (popmax 0.000254%, nfe) (gnomAD).

How is DK1-CDG inherited?

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

DOLK p.Val232del

c.684GGT[2] · rs1841674220 · VCV1004514

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000254%, nfe)

Conditions

DK1-congenital disorder of glycosylation

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.075	GERP -1.7, phastCons 0.56

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000254% European (non-Finnish) · 3/1,180,004 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000205% 3/1,461,890 alleles · very rare

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: DOLK
Protein: p.Val232del
Coding: c.684GGT[2]
MANE Select: NM_014908
dbSNP: rs1841674220
Type: Microsatellite
Location: chr9:128946612 (GRCh38)
Gene constraint: LOEUF 0.858 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.37

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

Disease context

DK1-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For DK1-CDG (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

DOLK p.Leu288del Uncertain significance ★★ same condition
DOLK p.Ile409fs Uncertain significance ★ same condition
DOLK p.Val232= Likely benign ★ same residue
DOLK p.His408Asp Pathogenic/Likely pathogenic ★★ same condition
DOLK p.Met1Ile Pathogenic/Likely pathogenic ★★ same condition
DOLK p.Met1Thr Pathogenic/Likely pathogenic ★★ same condition
DOLK c.-194G>T Uncertain significance ★★ same condition
DOLK c.-22G>A 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/dolk-p-val232del (accessed [today's date]).

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