Is VRK1 p.Arg3Phe (c.7_8delinsTT) pathogenic?

VRK1 p.Arg3Phe (c.78delinsTT) is classified Uncertain significance in VRK1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-06-28). No gnomAD frequency available for this variant; Associated with pontocerebellar hypoplasia type 1.

What condition is associated with VRK1 p.Arg3Phe (c.7_8delinsTT)?

VRK1 p.Arg3Phe (c.7_8delinsTT) is associated with pontocerebellar hypoplasia type 1 (ClinVar).

How common is VRK1 p.Arg3Phe (c.7_8delinsTT) in the general population?

VRK1 p.Arg3Phe (c.7_8delinsTT) is no gnomAD frequency available for this variant (gnomAD).

VRK1 p.Arg3Phe

c.7_8delinsTT · rs1566696565 · VCV574450

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

pontocerebellar hypoplasia type 1

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 5.9	GERP 2, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 14 kb · p 0.82 · regional, not allelic

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: VRK1
Protein: p.Arg3Phe
Coding: c.7_8delinsTT
MANE Select: NM_003384
dbSNP: rs1566696565
Type: Indel
Location: chr14:96833478 (GRCh38)
Gene constraint: LOEUF 0.747 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.37 · 26 PDB
Residue 3: a turn

Full VRK1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

pontocerebellar hypoplasia type 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

VRK1 p.Arg3Cys Uncertain significance ★★ ⚠ same residue
VRK1 p.Arg3_Val4insTer Pathogenic ★ same residue
VRK1 p.Arg3fs Likely pathogenic ★ same residue
VRK1 p.Arg3His Uncertain significance ★ ⚠ same residue
VRK1 p.Arg3= Likely benign ★ same residue
VRK1 c.161-3C>T Uncertain significance ★★ same condition
VRK1 p.Arg103Cys Uncertain significance ★★ ⚠ same condition
VRK1 p.Asn234Ser 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/vrk1-p-arg3phe (accessed [today's date]).

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