ANKS6 p.Ala52fs
c.154del · VCV3686362
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 1 of 15 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 5.6 | GERP -0.16, phastCons 1 |
| Region caveats | ||
| Repeat context | tandem | (CGGCCC)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No allele count reported in gnomAD v4.1 (AN 1,187,094). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- ANKS6
- Protein
- p.Ala52fs
- Coding
- c.154del
- MANE Select
- NM_173551
- Type
- Deletion
- Location
- chr9:98796338 (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 52
- the 'disordered' region
Disease context
nephronophthisis 16 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Nephronophthisis (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Adult, Antenatal, Childhood, Infancy, Neonatal
- Prevalence
- 1-9 / 100 000 (Finland)
Similar variants
- ANKS6 p.Ala52Val Uncertain significance ★★ ⚠ same residue
- ANKS6 p.Asp288fs Pathogenic/Likely pathogenic ★★ same condition
- ANKS6 p.Tyr790_Gln791delinsTer Pathogenic ★★ same condition
- ANKS6 c.2327-19del Benign/Likely benign ★★ same condition
- ANKS6 p.Ala145fs Pathogenic ★ same condition
- ANKS6 p.Ala64fs Pathogenic ★ same condition
- ANKS6 p.Glu44fs Pathogenic ★ same condition
- ANKS6 p.Leu180fs Pathogenic ★ same condition
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-ala52fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown