Is DOCK2 c.4644+12del pathogenic?

DOCK2 c.4644+12del is classified Likely benign in DOCK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-06-03). Absent from gnomAD; Associated with DOCK2 deficiency.

What condition is associated with DOCK2 c.4644+12del?

DOCK2 c.4644+12del is associated with DOCK2 deficiency (ClinVar).

How common is DOCK2 c.4644+12del in the general population?

DOCK2 c.4644+12del is absent from gnomAD (gnomAD).

DOCK2 c.4644+12del

Q: How is Combined immunodeficiency due to DOCK2 deficiency inherited?

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

rs2113868036 · VCV1563134

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

DOCK2 deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +12	near-intronic (+12 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.59	GERP 0.31, phastCons 0.001
Non-coding constraint	Z 3.75	1 kb window · o/e 0.74 · 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: DOCK2
Coding: c.4644+12del
MANE Select: NM_004946
dbSNP: rs2113868036
Type: Deletion
Location: chr5:170067698 (GRCh38)
Gene constraint: LOEUF 0.421 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 80.40 · 6 PDB

Full DOCK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DOCK2 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Combined immunodeficiency due to DOCK2 deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

DOCK2 c.1843+9del Likely benign ★★ same condition
DOCK2 c.1057del Likely pathogenic ★ same condition
DOCK2 p.Gly616fs Pathogenic ★ same condition
DOCK2 p.His907fs Pathogenic ★ same condition
DOCK2 p.Lys872fs Likely pathogenic ★ same condition
DOCK2 p.Met450fs Pathogenic ★ same condition
DOCK2 c.2031+3_2031+4del Uncertain significance ★ same condition
DOCK2 p.Asn920_Val923del 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/dock2-c-4644-plus-12del (accessed [today's date]).

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