AMELX p.Ile112=
c.336C>A · rs756968232 · VCV747013
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.079%, amr)
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 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 9.149 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.079%
Admixed American · 36/45,563 alleles
Filtering AF
0.0586%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0516%
Overall
0.00298%
36/1,208,630 alleles · ultra-rare
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.Ile112=
- Coding
- c.336C>A
- MANE Select
- NM_001142
- dbSNP
- rs756968232
- Type
- single nucleotide variant
- Location
- chrX:11298739 (GRCh38)
- Structure
- AlphaFold pLDDT 59.51
- Residue 112
- the 'disordered' region
Similar variants
- AMELX p.Met1Ile Likely pathogenic ★★ same type
- AMELX p.Pro56Thr Pathogenic/Likely pathogenic ★★ ⚠ same type
- AMELX c.103-111A>G Uncertain significance ★★ same type
- AMELX c.54+65T>C Benign ★★ same type
- AMELX p.His73= Benign ★★ same type
- AMELX c.103-1G>A Likely pathogenic ★ same type
- AMELX c.144+1G>A Likely pathogenic ★ same type
- AMELX p.Gln141Ter Likely pathogenic ★ 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-ile112 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown