ANKS3 p.Ala506=
c.1518T>C · VCV3400072
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0269%, 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 -20 | GERP -3.3 |
| Overall | ||
| CADD | 0.007 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0269%
Admixed American · 16/59,530 alleles
Filtering AF
0.0169%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0137%
Overall
0.00261%
42/1,607,446 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0269% | 3,721 |
| African / African-American | 0.0253% | 3,947 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,114 |
| European (non-Finnish) | 0.000425% | 235,362 |
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
- ANKS3
- Protein
- p.Ala506=
- Coding
- c.1518T>C
- MANE Select
- NM_133450
- Type
- single nucleotide variant
- Location
- chr16:4698833 (GRCh38)
- Gene constraint
- LOEUF 1.102 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.94 · 2 PDB
Similar variants
- ANKS3 p.Cys168Gly Likely benign ★★ same type
- ANKS3 p.Glu328= Benign ★★ same type
- ANKS3 p.Gly25Glu Benign ★★ same type
- ANKS3 p.His377= Benign ★★ same type
- ANKS3 p.Leu14= Benign/Likely benign ★★ same type
- ANKS3 p.Val585= Benign ★★ same type
- ANKS3 p.Ala118Thr Uncertain significance ★ same type
- ANKS3 p.Ala271Thr 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/anks3-p-ala506 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown