SPTLC2 p.Val72=
c.216G>A · VCV4922687
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000847%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.111 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.13 | GERP -3.8, phastCons 0.45 |
| Overall | ||
| CADD | 8.382 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000847%
European (non-Finnish) · 10/1,180,032 alleles
Filtering AF
0.000429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000312%
Overall
0.00062%
10/1,614,194 alleles · very rare
exomes 10/1,461,882 · genomes 0/152,312 · joint denominator
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
- SPTLC2
- Protein
- p.Val72=
- Coding
- c.216G>A
- MANE Select
- NM_004863
- Type
- single nucleotide variant
- Location
- chr14:77597297 (GRCh38)
- Gene constraint
- LOEUF 0.494 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 86.47 · 17 PDB
- Residue 72
- an α-helix
Similar variants
- SPTLC2 p.Arg183Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
- SPTLC2 p.Gly382Val Pathogenic/Likely pathogenic ★★ same type
- SPTLC2 p.Ser384Phe Pathogenic/Likely pathogenic ★★ ⚠ same type
- SPTLC2 c.1176+6C>T Uncertain significance ★★ same type
- SPTLC2 c.1439+3A>G Uncertain significance ★★ same type
- SPTLC2 c.756+3A>G Uncertain significance ★★ same type
- SPTLC2 c.-160A>G Uncertain significance ★★ same type
- SPTLC2 c.*100G>A 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/sptlc2-p-val72 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown