SMS p.Ala36=
c.108G>A · VCV3714274
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00528%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.087 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -4.6 | GERP -4.2 |
| Overall | ||
| CADD | 0.729 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00528%
South Asian · 3/56,864 alleles
Filtering AF
0.0014%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000688%
Overall
0.000912%
10/1,096,182 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00528% | 18,955 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,540 |
| European (non-Finnish) | 0.000671% | 148,935 |
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
- SMS
- Protein
- p.Ala36=
- Coding
- c.108G>A
- MANE Select
- NM_004595
- Type
- single nucleotide variant
- Location
- chrX:21967254 (GRCh38)
- Structure
- AlphaFold pLDDT 95.09 · 2 PDB
- Residue 36
- a β-strand
Similar variants
- SMS p.Ala36Val Likely benign ★★ same residue
- SMS p.Arg234Ter Pathogenic/Likely pathogenic ★★ same type
- SMS p.Gly203Asp Pathogenic ★★ same type
- SMS p.Gly56Ser Pathogenic ★★ ⚠ same type
- SMS p.Ile196Thr Likely pathogenic ★★ same type
- SMS p.Pro112Leu Pathogenic/Likely pathogenic ★★ ⚠ same type
- SMS c.1061+2T>C Uncertain significance ★★ same type
- SMS c.505+3A>G 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/sms-p-ala36 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown