ANKS3 p.Val585=
c.1755G>C · rs34901190 · VCV775368
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 5.19%, afr) — too common for a highly-penetrant pathogenic allele
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 0.58 | GERP 1.5, phastCons 0.1 |
| Overall | ||
| CADD | 1.593 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.19%
African / African-American · 3,896/74,998 alleles
Filtering AF
5.06%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5%
Overall
0.273%
4,399/1,609,750 alleles · common
exomes 2,110/1,457,418 · genomes 2,289/152,332 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.19% | 19 |
| Remaining individualsnot grpmax-eligible | 0.344% | 291 |
| Admixed American | 0.342% | 292 |
| Middle Eastern | 0.165% | 605 |
| South Asian | 0.0133% | 7,523 |
| East Asian | 0.00893% | 11,198 |
| European (non-Finnish) | 0.00501% | 19,979 |
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.Val585=
- Coding
- c.1755G>C
- MANE Select
- NM_133450
- dbSNP
- rs34901190
- Type
- single nucleotide variant
- Location
- chr16:4698032 (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.Ala118Thr Uncertain significance ★ same type
- ANKS3 p.Ala271Thr Uncertain significance ★ ⚠ same type
- ANKS3 p.Ala431Val 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-val585 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown