Is CAMK2A c.65del pathogenic?

CAMK2A c.65del is classified Likely pathogenic in CAMK2A (ClinVar, No assertion criteria, 1 submitter; last evaluated 2017-07-03). Absent from gnomAD; Associated with intellectual disability.

What condition is associated with CAMK2A c.65del?

CAMK2A c.65del is associated with intellectual disability (ClinVar).

How common is CAMK2A c.65del in the general population?

CAMK2A c.65del is absent from gnomAD (gnomAD).

CAMK2A c.65del

rs1554123982 · VCV430911

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

intellectual disability

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 1.2	GERP -1.8, phastCons 1
Non-coding constraint	Z -0.17	1 kb window · o/e 1.01 · regional · uncalibrated

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: CAMK2A
Coding: c.65del
MANE Select: NM_015981 · reported on NM_171825
dbSNP: rs1554123982
Type: Deletion
Location: chr5:150273157 (GRCh38)
Gene constraint: LOEUF 0.187 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 86.44 · 22 PDB

Full CAMK2A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

intellectual disability — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CAMK2A p.Pro212Leu Pathogenic ★★ same condition
CAMK2A c.1237+1G>A Conflicting classifications of pathogenicity ★ ⚠ same condition
CAMK2A p.Pro235Leu Conflicting classifications of pathogenicity ★ ⚠ same condition
CAMK2A c.598+2dup Likely pathogenic same condition
CAMK2A p.Glu109Asp Pathogenic same condition
CAMK2A p.Glu183Val Pathogenic same condition
CAMK2A p.His282Arg Pathogenic same condition
CAMK2A p.Phe98Ser 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/camk2a-c-65del (accessed [today's date]).

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