PLA2G6 p.Pro155=
c.465C>A · rs2089029529 · VCV2863221
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
neurodegeneration with brain iron accumulation 2A
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.104 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -3.9 | GERP -5.1 |
| Overall | ||
| CADD | 6.997 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PLA2G6
- Protein
- p.Pro155=
- Coding
- c.465C>A
- MANE Select
- NM_003560
- dbSNP
- rs2089029529
- Type
- single nucleotide variant
- Location
- chr22:38143249 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.16
Disease context
neurodegeneration with brain iron accumulation 2A — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Infantile neuroaxonal dystrophy (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- PLA2G6 p.Pro155Leu Uncertain significance ★ ⚠ same residue
- PLA2G6 c.1078-1G>A Likely pathogenic ★★ same condition
- PLA2G6 c.1186+1G>A Pathogenic/Likely pathogenic ★★ same condition
- PLA2G6 c.1186+1G>T Pathogenic/Likely pathogenic ★★ same condition
- PLA2G6 c.1187-1G>A Pathogenic/Likely pathogenic ★★ same condition
- PLA2G6 c.1349-2A>G Pathogenic/Likely pathogenic ★★ same condition
- PLA2G6 c.1427+1G>A Pathogenic/Likely pathogenic ★★ same condition
- PLA2G6 c.1592-2A>C Pathogenic/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/pla2g6-p-pro155 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown