Is AHNAK2 p.Gln2136Asp (c.6406_6408delinsGAC) pathogenic?

AHNAK2 p.Gln2136Asp (c.64066408delinsGAC) is classified Uncertain significance in AHNAK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-01-01). No gnomAD frequency available for this variant; Associated with migraine disorder.

What condition is associated with AHNAK2 p.Gln2136Asp (c.6406_6408delinsGAC)?

AHNAK2 p.Gln2136Asp (c.6406_6408delinsGAC) is associated with migraine disorder, hereditary episodic ataxia (ClinVar).

How common is AHNAK2 p.Gln2136Asp (c.6406_6408delinsGAC) in the general population?

AHNAK2 p.Gln2136Asp (c.6406_6408delinsGAC) is no gnomAD frequency available for this variant (gnomAD).

How is Hypnic headache inherited?

Typically Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

AHNAK2 p.Gln2136Asp

c.6406_6408delinsGAC · rs1898490907 · VCV983126

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

migraine disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.39	GERP 0.29, phastCons 0.001
Regional constraint	o/e 1.23	unconstrained · MANE · 32 kb · p 4.7e-50 · regional, not allelic
Region caveats
Repeat context	tandem	chr14:104943070 segmental duplication, simple repeat · ambiguous alignment · reads may not map uniquely · confidence, not pathogenicity

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: AHNAK2
Protein: p.Gln2136Asp
Coding: c.6406_6408delinsGAC
MANE Select: NM_138420
dbSNP: rs1898490907
Type: Indel
Location: chr14:104949043 (GRCh38)
Gene constraint: LOEUF 0.917 · pLI <0.01 (gnomAD)

Full AHNAK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

migraine disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary episodic ataxia

For Hypnic headache (Orphanet):

Inheritance: Not applicable
Onset: Adult, Childhood, Elderly

Similar variants

AHNAK2 p.Gln2136His Uncertain significance ★ ⚠ same residue
AHNAK2 p.Leu2333Pro Likely benign ★ same type

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/ahnak2-p-gln2136asp (accessed [today's date]).

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