SPPL2A p.Phe130=
c.390T>C · rs1270326415 · VCV1618632
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 1,509,236)
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 6 | GERP 2.4, phastCons 1 |
| Overall | ||
| CADD | 11.91 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,509,236). 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
- SPPL2A
- Protein
- p.Phe130=
- Coding
- c.390T>C
- MANE Select
- NM_032802
- dbSNP
- rs1270326415
- Type
- single nucleotide variant
- Location
- chr15:50748173 (GRCh38)
- Gene constraint
- LOEUF 1.074 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 79.28 · 2 PDB
- Residue 130
- the pa domain
Similar variants
- SPPL2A p.Ala179Val Uncertain significance ★★ ⚠ same type
- SPPL2A p.Ala298Val Uncertain significance ★★ ⚠ same type
- SPPL2A p.Ala480Thr Uncertain significance ★★ ⚠ same type
- SPPL2A p.Arg281Cys Uncertain significance ★★ ⚠ same type
- SPPL2A p.Arg281His Uncertain significance ★★ ⚠ same type
- SPPL2A p.Arg424Thr Uncertain significance ★★ ⚠ same type
- SPPL2A p.Arg483His Uncertain significance ★★ same type
- SPPL2A p.Asn66Thr Uncertain significance ★★ ⚠ same type
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/sppl2a-p-phe130 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown