ANKS6 p.Pro694=
c.2082G>A · rs755118485 · VCV3041703
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0169%, mid)
Conditions
1
ANKS6-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.067 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -4.3 |
| Overall | ||
| CADD | 0.021 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0169%
Middle Eastern · 1/5,924 alleles
Filtering AF
0.00122%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.00178%
26/1,461,262 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0169% | 5,924 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,232 |
| European (non-Finnish) | 0.00186% | 53,632 |
| South Asian | 0.0011% | 91,004 |
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
- ANKS6
- Protein
- p.Pro694=
- Coding
- c.2082G>A
- MANE Select
- NM_173551
- dbSNP
- rs755118485
- Type
- single nucleotide variant
- Location
- chr9:98768141 (GRCh38)
- Gene constraint
- LOEUF 0.869 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 60.60 · 1 PDB
- Residue 694
- the 'disordered' region
Disease context
ANKS6-related disorder
Similar variants
- ANKS6 p.Pro694Ser Uncertain significance ★★ ⚠ same residue
- ANKS6 p.Arg412Ter Likely pathogenic ★ same condition
- ANKS6 p.His436Gln Uncertain significance ⚠ same condition
- ANKS6 c.1220-4A>C Likely benign same condition
- ANKS6 p.Gln791= Likely benign same condition
- ANKS6 p.Leu787= Likely benign same condition
- ANKS6 p.Lys286= Likely benign same condition
- ANKS6 c.1973-3C>G Pathogenic/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/anks6-p-pro694 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown