AMELX p.Pro122=
c.366C>T · rs147013110 · VCV3042941
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.433%, afr)
Conditions
1
AMELX-related disorder
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 -3.5 | GERP -1.2 |
| Overall | ||
| CADD | 2.197 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.433%
African / African-American · 246/56,800 alleles
Filtering AF
0.389%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.371%
Overall
0.0261%
316/1,208,785 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.433% | 231 |
| Middle Eastern | 0.275% | 363 |
| Remaining individualsnot grpmax-eligible | 0.0357% | 2,799 |
| Admixed American | 0.0241% | 4,145 |
| South Asian | 0.00706% | 14,165 |
| European (non-Finnish) | 0.00279% | 35,798 |
| Finnishnot grpmax-eligible | 0.00215% | 46,437 |
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
- AMELX
- Protein
- p.Pro122=
- Coding
- c.366C>T
- MANE Select
- NM_001142
- dbSNP
- rs147013110
- Type
- single nucleotide variant
- Location
- chrX:11298769 (GRCh38)
- Structure
- AlphaFold pLDDT 59.51
- Residue 122
- the 'disordered' region
Disease context
AMELX-related disorder
Similar variants
- AMELX p.Met1Ile Likely pathogenic ★★ same condition
- AMELX p.Pro56Thr Pathogenic/Likely pathogenic ★★ ⚠ same condition
- AMELX c.103-1G>A Likely pathogenic ★ same condition
- AMELX p.Gln141Ter Likely pathogenic ★ same condition
- AMELX p.Pro75= Likely benign same condition
- AMELX c.103-111A>G Uncertain significance ★★ same type
- AMELX c.54+65T>C Benign ★★ same type
- AMELX p.His73= Benign ★★ 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/amelx-p-pro122 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown