APEX2 p.Ala83=
c.249C>T · rs61752443 · VCV719560
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.25%, nfe)
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 -0.61 | GERP -2, phastCons 0.021 |
| Overall | ||
| CADD | 7.493 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.25%
European (non-Finnish) · 11,126/888,106 alleles
Filtering AF
1.23%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.23%
Overall
1.01%
12,082/1,193,051 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.25% | 80 |
| Remaining individualsnot grpmax-eligible | 0.801% | 125 |
| Admixed American | 0.789% | 127 |
| Finnishnot grpmax-eligible | 0.199% | 502 |
| African / African-American | 0.176% | 568 |
| South Asian | 0.0888% | 1,126 |
| Middle Eastern | 0.0238% | 4,199 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00483% | 20,698 |
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
- APEX2
- Protein
- p.Ala83=
- Coding
- c.249C>T
- MANE Select
- NM_014481
- dbSNP
- rs61752443
- Type
- single nucleotide variant
- Location
- chrX:55002258 (GRCh38)
- Structure
- AlphaFold pLDDT 78.87
Similar variants
- APEX2 p.Ala309= Benign ★★ same type
- APEX2 p.Arg141Cys Likely benign ★★ same type
- APEX2 p.Ala126Ser Uncertain significance ★ ⚠ same type
- APEX2 p.Ala160Val Uncertain significance ★ ⚠ same type
- APEX2 p.Ala267Thr Uncertain significance ★ ⚠ same type
- APEX2 p.Ala29Ser Uncertain significance ★ ⚠ same type
- APEX2 p.Ala372Gly Uncertain significance ★ ⚠ same type
- APEX2 p.Arg125Trp 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/apex2-p-ala83 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown