LRRK2 p.Ser1007=
c.3021T>C · rs55783828 · VCV1798928
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0527%, sas)
Conditions
1
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 0.42 | GERP -3.1, phastCons 1 |
| Overall | ||
| CADD | 7.445 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0527%
South Asian · 48/91,090 alleles
Filtering AF
0.0408%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0366%
Overall
0.0031%
50/1,613,950 alleles · ultra-rare
exomes 49/1,461,740 · genomes 1/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0527% | 1,898 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,237 |
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
- LRRK2
- Protein
- p.Ser1007=
- Coding
- c.3021T>C
- MANE Select
- NM_198578
- dbSNP
- rs55783828
- Type
- single nucleotide variant
- Location
- chr12:40295569 (GRCh38)
- Gene constraint
- LOEUF 0.778 · pLI <0.01 · ClinGen HI dosage-sensitivity unlikely (gnomAD)
- Structure
- AlphaFold pLDDT 77.64 · 58 PDB
- Residue 1007
- a turn
Similar variants
- LRRK2 p.Ser1007Asn 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
- LRRK2 p.Ala233Val 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-ser1007 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown