SMS p.Asp142=
c.426C>T · rs185114683 · VCV2899131
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0923%, mid)
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 -0.44 | GERP -2.9, phastCons 0.18 |
| Overall | ||
| CADD | 3.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0923%
Middle Eastern · 4/4,336 alleles
Filtering AF
0.0314%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.019%
Overall
0.00357%
43/1,203,970 alleles · ultra-rare
exomes 36/1,091,652 · genomes 7/112,318 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0923% | 1,084 |
| Admixed American | 0.0109% | 9,156 |
| African / African-American | 0.00873% | 11,451 |
| South Asian | 0.00529% | 18,892 |
| Remaining individualsnot grpmax-eligible | 0.00422% | 23,714 |
| East Asian | 0.00296% | 33,770 |
| European (non-Finnish) | 0.00259% | 38,670 |
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.Asp142=
- Coding
- c.426C>T
- MANE Select
- NM_004595
- dbSNP
- rs185114683
- Type
- single nucleotide variant
- Location
- chrX:21977157 (GRCh38)
- Structure
- AlphaFold pLDDT 95.09 · 2 PDB
- Residue 142
- the pabs domain; a β-strand
Similar variants
- 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
- SMS c.661-4G>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/sms-p-asp142 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown