Is ANKS6 p.Gln791= (c.2373G>A) pathogenic?

ANKS6 p.Gln791= (c.2373G>A) is classified Likely benign in ANKS6 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-08-05). Very rare (popmax 0.00168%, amr); Associated with ANKS6-related disorder.

What condition is associated with ANKS6 p.Gln791= (c.2373G>A)?

ANKS6 p.Gln791= (c.2373G>A) is associated with ANKS6-related disorder (ClinVar).

How common is ANKS6 p.Gln791= (c.2373G>A) in the general population?

ANKS6 p.Gln791= (c.2373G>A) is very rare (popmax 0.00168%, amr) (gnomAD).

ANKS6 p.Gln791=

c.2373G>A · VCV3355799

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00168%, amr)

Conditions

ANKS6-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.073	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.2	GERP 2.3, phastCons 1
Overall
CADD	8.308	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00168% Admixed American · 1/59,484 alleles

Overall 0.000124% 2/1,610,242 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00168%	59,484
Remaining individualsnot grpmax-eligible	0.0016%	62,396

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.Gln791=
Coding: c.2373G>A
MANE Select: NM_173551
Type: single nucleotide variant
Location: chr9:98751050 (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 791: the sam domain; an α-helix

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

Disease context

ANKS6-related disorder

Similar variants

ANKS6 p.Gln791Arg Uncertain significance ★ ⚠ same residue
ANKS6 p.Gln791His 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.Leu787= Likely benign same condition
ANKS6 p.Lys286= Likely benign same condition
ANKS6 p.Pro694= Likely benign 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-gln791 (accessed [today's date]).

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