ANKS6 p.Lys438=
c.1314G>A · VCV4723126
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
nephronophthisis 16
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 2.6 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 8.881 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ANKS6
- Protein
- p.Lys438=
- Coding
- c.1314G>A
- MANE Select
- NM_173551
- Type
- single nucleotide variant
- Location
- chr9:98780243 (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 438
- 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 c.1973-3C>G Pathogenic/Likely pathogenic ★★ same condition
- ANKS6 p.Arg461Ter Pathogenic/Likely pathogenic ★★ same condition
- ANKS6 c.907+6C>T Uncertain significance ★★ same condition
- ANKS6 p.Ala215Thr Uncertain significance ★★ ⚠ same condition
- ANKS6 p.Ala215Val Uncertain significance ★★ ⚠ same condition
- ANKS6 p.Ala249Thr Uncertain significance ★★ ⚠ same condition
- ANKS6 p.Ala261Thr Uncertain significance ★★ ⚠ same condition
- ANKS6 p.Ala350Thr Uncertain significance ★★ ⚠ 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-lys438 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown