Is ANKS6 p.Pro564Thr (c.1690C>A) pathogenic?

ANKS6 p.Pro564Thr (c.1690C>A) is classified Likely benign in ANKS6 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-06-03). AlphaMissense: ambiguous (0.5453); Rare (popmax 0.405%, eas); Associated with nephronophthisis 16.

What condition is associated with ANKS6 p.Pro564Thr (c.1690C>A)?

ANKS6 p.Pro564Thr (c.1690C>A) is associated with nephronophthisis 16 (ClinVar).

How common is ANKS6 p.Pro564Thr (c.1690C>A) in the general population?

ANKS6 p.Pro564Thr (c.1690C>A) is rare (popmax 0.405%, eas) (gnomAD).

How is Nephronophthisis inherited?

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

What do computational predictors say about ANKS6 p.Pro564Thr (c.1690C>A)?

AlphaMissense predicts ambiguous (score 0.5453) — an in-silico prediction, not a clinical call.

ANKS6 p.Pro564Thr

c.1690C>A · rs190075616 · VCV767308

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

ambiguous

0.5453 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.405%, eas)

Conditions

nephronophthisis 16

Computational evidence

Protein change
AlphaMissense	0.5453	ambiguous
REVEL	0.617	indeterminate
SaProt	LLR -7.06	tolerated
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.27 · evaluated, not missing
Constraint at this position
Conservation	phyloP 9.6	GERP 2.2, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 60 kb · p 0.79 · regional, not allelic
Overall
CADD	24.1	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.405% East Asian · 171/42,246 alleles

Filtering AF 0.355% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.336%

Overall 0.0243% 385/1,583,294 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.405%	247
South Asian	0.0574%	1,741
Remaining individualsnot grpmax-eligible	0.0343%	2,914
European (non-Finnish)	0.0121%	8,268
Admixed American	0.00355%	28,140

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.Pro564Thr
Coding: c.1690C>A
MANE Select: NM_173551
dbSNP: rs190075616
Type: single nucleotide variant
Location: chr9:98774008 (GRCh38)
Gene constraint: LOEUF 0.869 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 60.60 · 1 PDB

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.Pro564Ala Uncertain significance ★★ ⚠ same residue
ANKS6 p.Pro564Ser Uncertain significance ★ ⚠ same residue
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

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-pro564thr (accessed [today's date]).

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