Is LRRK2 p.Val239= (c.717G>A) pathogenic?

LRRK2 p.Val239= (c.717G>A) is classified Likely benign in LRRK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-05-02). No allele count reported in gnomAD v4.1 (AN 1,611,378); Associated with Inborn genetic diseases.

What condition is associated with LRRK2 p.Val239= (c.717G>A)?

LRRK2 p.Val239= (c.717G>A) is associated with Inborn genetic diseases (ClinVar).

How common is LRRK2 p.Val239= (c.717G>A) in the general population?

LRRK2 p.Val239= (c.717G>A) is no allele count reported in gnomAD v4.1 (AN 1,611,378) (gnomAD).

LRRK2 p.Val239=

c.717G>A · rs1941836533 · VCV1757523

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 1,611,378)

Conditions

Inborn genetic diseases

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 0.13	GERP -3.8, phastCons 0.98
Overall
CADD	3.595	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,611,378). 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: LRRK2
Protein: p.Val239=
Coding: c.717G>A
MANE Select: NM_198578
dbSNP: rs1941836533
Type: single nucleotide variant
Location: chr12:40243560 (GRCh38)
Gene constraint: LOEUF 0.778 · pLI <0.01 · ClinGen HI dosage-sensitivity unlikely (gnomAD)
Structure: AlphaFold pLDDT 77.64 · 58 PDB
Residue 239: an α-helix; the 'required for rab29-mediated activation' region

Full LRRK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

LRRK2 p.Val239Leu Uncertain significance ★ ⚠ same residue
LRRK2 p.Val239Met Uncertain significance ★ ⚠ same residue
LRRK2 p.Ala1396Ser Uncertain significance ★★ ⚠ same condition
LRRK2 p.Ala1413Glu Uncertain significance ★★ ⚠ same condition
LRRK2 p.Ala1430Val Uncertain significance ★★ ⚠ same condition
LRRK2 p.Ala1440Val Uncertain significance ★★ same condition
LRRK2 p.Ala1572Thr Uncertain significance ★★ ⚠ same condition
LRRK2 p.Ala1659Gly 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/lrrk2-p-val239 (accessed [today's date]).

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