Is ANKS6 p.Phe567fs (c.1683_1698dup) pathogenic?

ANKS6 p.Phe567fs (c.16831698dup) is classified Pathogenic in ANKS6 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-04). Absent from gnomAD; Associated with nephronophthisis 16.

What condition is associated with ANKS6 p.Phe567fs (c.1683_1698dup)?

ANKS6 p.Phe567fs (c.1683_1698dup) is associated with nephronophthisis 16 (ClinVar).

How common is ANKS6 p.Phe567fs (c.1683_1698dup) in the general population?

ANKS6 p.Phe567fs (c.1683_1698dup) is absent from gnomAD (gnomAD).

How is Nephronophthisis inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

ANKS6 p.Phe567fs

c.1683_1698dup · rs2490390282 · VCV2883386

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

nephronophthisis 16

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 9 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.2, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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.Phe567fs
Coding: c.1683_1698dup
MANE Select: NM_173551
dbSNP: rs2490390282
Type: Duplication
Location: chr9:98773999 (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 567: the 'disordered' region

Full ANKS6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

nephronophthisis 16 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Nephronophthisis (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Antenatal, Childhood, Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Finland)

Similar variants

ANKS6 p.Phe567= Likely benign ★ same residue
ANKS6 c.2327-19dup Benign/Likely benign ★★ same condition
ANKS6 p.Asn218fs Pathogenic ★ same condition
ANKS6 p.Gln504fs Pathogenic ★ same condition
ANKS6 p.Gly122fs Likely pathogenic ★ same condition
ANKS6 p.Pro559fs Pathogenic ★ same condition
ANKS6 p.Thr808fs Likely pathogenic ★ same condition
ANKS6 p.Val160fs Likely 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-phe567fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown