AMELX p.Val190=
c.570G>C · rs779785692 · VCV757487
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0895%, 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 7.3 | GERP 0.87, phastCons 1 |
| Overall | ||
| CADD | 15.58 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0895%
Admixed American · 41/45,803 alleles
Filtering AF
0.0678%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0602%
Overall
0.00383%
42/1,095,389 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0895% | 1,117 |
| Remaining individualsnot grpmax-eligible | 0.00211% | 47,480 |
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.Val190=
- Coding
- c.570G>C
- MANE Select
- NM_001142
- dbSNP
- rs779785692
- Type
- single nucleotide variant
- Location
- chrX:11298973 (GRCh38)
- Structure
- AlphaFold pLDDT 59.51
- Residue 190
- 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-val190 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown