AMOT p.Ser780=
c.2340G>A · rs149909515 · VCV777823
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.11%, 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 -1.1 | GERP -4.2, phastCons 0.004 |
| Overall | ||
| CADD | 2.114 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.11%
African / African-American · 1,210/57,381 alleles
Filtering AF
2.01%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.97%
Overall
0.117%
1,417/1,210,430 alleles · low-frequency
exomes 703/1,098,115 · genomes 714/112,315 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.11% | 47 |
| Admixed American | 0.21% | 477 |
| Remaining individualsnot grpmax-eligible | 0.181% | 554 |
| Middle Eastern | 0.046% | 2,176 |
| European (non-Finnish) | 0.00257% | 38,927 |
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.Ser780=
- Coding
- c.2340G>A
- MANE Select
- NM_001113490
- dbSNP
- rs149909515
- Type
- single nucleotide variant
- Location
- chrX:112781019 (GRCh38)
- Structure
- AlphaFold pLDDT 58.16 · 18 PDB
Similar variants
- AMOT p.Ser780Leu Uncertain significance ★ ⚠ same residue
- AMOT p.Ser780Thr Uncertain significance ★ ⚠ same residue
- AMOT p.Ala1032Val Benign ★★ same type
- AMOT p.Ser316= Benign ★★ same type
- AMOT p.Ser538= Benign ★★ same type
- AMOT p.Thr899Ala Benign ★★ same type
- AMOT p.Gln642His Likely pathogenic ★ ⚠ same type
- AMOT p.Ala1023Pro 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-ser780 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown