Is DOCK2 p.Thr354= (c.1062A>G) pathogenic?

DOCK2 p.Thr354= (c.1062A>G) is classified Benign/Likely benign in DOCK2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-19). Rare (popmax 0.177%, afr); Associated with DOCK2 deficiency.

What condition is associated with DOCK2 p.Thr354= (c.1062A>G)?

DOCK2 p.Thr354= (c.1062A>G) is associated with DOCK2 deficiency (ClinVar).

How common is DOCK2 p.Thr354= (c.1062A>G) in the general population?

DOCK2 p.Thr354= (c.1062A>G) is rare (popmax 0.177%, afr) (gnomAD).

DOCK2 p.Thr354=

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.1062A>G · rs143288655 · VCV725277

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.177%, afr)

Conditions

DOCK2 deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.18	GERP -3.9, phastCons 0.24
Overall
CADD	6.896	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.177% African / African-American · 133/75,036 alleles

Filtering AF 0.153% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.143%

Overall 0.00979% 158/1,613,316 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.177%	564
Admixed American	0.02%	4,996
Middle Eastern	0.0165%	6,046
Remaining individualsnot grpmax-eligible	0.016%	6,249
European (non-Finnish)	0.00017%	589,783

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.Thr354=
Coding: c.1062A>G
MANE Select: NM_004946
dbSNP: rs143288655
Type: single nucleotide variant
Location: chr5:169699388 (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 p.Thr354Ala Uncertain significance ★ ⚠ same residue
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

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-thr354 (accessed [today's date]).

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