AMOT p.Ser316=
c.948T>C · rs143986904 · VCV720806
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.12%, afr)
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 -0.15 | GERP -3.7, phastCons 0.008 |
| Overall | ||
| CADD | 4.948 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.12%
African / African-American · 2,278/55,302 alleles
Filtering AF
3.98%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.92%
Overall
0.226%
2,632/1,164,994 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.12% | 24 |
| Middle Eastern | 0.302% | 331 |
| Remaining individualsnot grpmax-eligible | 0.283% | 353 |
| Admixed American | 0.271% | 369 |
| South Asian | 0.0248% | 4,032 |
| European (non-Finnish) | 0.0108% | 9,283 |
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
- AMOT
- Protein
- p.Ser316=
- Coding
- c.948T>C
- MANE Select
- NM_001113490
- dbSNP
- rs143986904
- Type
- single nucleotide variant
- Location
- chrX:112815802 (GRCh38)
- Structure
- AlphaFold pLDDT 58.16 · 18 PDB
- Residue 316
- the 'disordered' region
Similar variants
- AMOT p.Ser316Phe Uncertain significance ★ ⚠ same residue
- AMOT p.Ala1032Val Benign ★★ same type
- AMOT p.Ser538= Benign ★★ same type
- AMOT p.Ser780= Benign ★★ same type
- AMOT p.Thr899Ala Benign ★★ same type
- AMOT p.Gln642His Likely pathogenic ★ ⚠ same type
- AMOT p.Ala1023Pro Uncertain significance ★ ⚠ same type
- AMOT p.Ala460Gly 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/amot-p-ser316 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown