SMS p.Arg110=
c.330A>G · rs142264016 · VCV212274
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.145%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.091 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.25 | GERP -4.3, phastCons 0.56 |
| Overall | ||
| CADD | 6.36 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.145%
African / African-American · 83/57,256 alleles
Filtering AF
0.12%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.11%
Overall
0.00737%
89/1,207,732 alleles · rare
exomes 41/1,095,555 · genomes 48/112,177 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.145% | 690 |
| Remaining individualsnot grpmax-eligible | 0.00631% | 15,844 |
| Admixed American | 0.00437% | 22,884 |
| European (non-Finnish) | 0.000112% | 892,953 |
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.Arg110=
- Coding
- c.330A>G
- MANE Select
- NM_004595
- dbSNP
- rs142264016
- Type
- single nucleotide variant
- Location
- chrX:21977061 (GRCh38)
- Structure
- AlphaFold pLDDT 95.09 · 2 PDB
Similar variants
- SMS p.Arg110Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
- SMS p.Arg110Gly Likely pathogenic ⚠ 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
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-arg110 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown