Is DOCK2 p.Thr459= (c.1377G>A) pathogenic?

DOCK2 p.Thr459= (c.1377G>A) is classified Likely benign in DOCK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-06). Ultra-rare (popmax 0.0982%, eas); Associated with DOCK2 deficiency.

What condition is associated with DOCK2 p.Thr459= (c.1377G>A)?

DOCK2 p.Thr459= (c.1377G>A) is associated with DOCK2 deficiency (ClinVar).

How common is DOCK2 p.Thr459= (c.1377G>A) in the general population?

DOCK2 p.Thr459= (c.1377G>A) is ultra-rare (popmax 0.0982%, eas) (gnomAD).

DOCK2 p.Thr459=

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

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

c.1377G>A · rs144520292 · VCV1092202

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0982%, eas)

Conditions

DOCK2 deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -1.4	GERP -0.92
Overall
CADD	5.789	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0982% East Asian · 44/44,810 alleles

Filtering AF 0.0751% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.067%

Overall 0.00645% 104/1,613,514 alleles · ultra-rare exomes 95/1,461,222 · genomes 9/152,292 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0982%	1,018
South Asian	0.0176%	5,691
Remaining individualsnot grpmax-eligible	0.0064%	15,620
Admixed American	0.005%	20,003
African / African-American	0.004%	25,006
European (non-Finnish)	0.00288%	34,695

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: DOCK2
Protein: p.Thr459=
Coding: c.1377G>A
MANE Select: NM_004946
dbSNP: rs144520292
Type: single nucleotide variant
Location: chr5:169702421 (GRCh38)
Gene constraint: LOEUF 0.421 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 80.40 · 6 PDB
Residue 459: the c2 dock-type domain

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.2267+3G>A Uncertain significance ★★ same condition
DOCK2 c.2704-3C>T Uncertain significance ★★ same condition
DOCK2 c.4467+4A>G Uncertain significance ★★ same condition
DOCK2 p.Ala1393Val Uncertain significance ★★ ⚠ same condition
DOCK2 p.Ala1710Val Uncertain significance ★★ ⚠ same condition
DOCK2 p.Ala1765Val Uncertain significance ★★ ⚠ same condition
DOCK2 p.Ala24Pro Uncertain significance ★★ ⚠ same condition
DOCK2 p.Ala454Val 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-p-thr459 (accessed [today's date]).

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