Is DOCK2 p.Met535Val (c.1603A>G) pathogenic?

DOCK2 p.Met535Val (c.1603A>G) is classified Conflicting classifications of pathogenicity in DOCK2 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2026-01-04). AlphaMissense: ambiguous (0.3994); Rare (popmax 0.182%, mid); Associated with DOCK2 deficiency.

What condition is associated with DOCK2 p.Met535Val (c.1603A>G)?

DOCK2 p.Met535Val (c.1603A>G) is associated with DOCK2 deficiency (ClinVar).

How common is DOCK2 p.Met535Val (c.1603A>G) in the general population?

DOCK2 p.Met535Val (c.1603A>G) is rare (popmax 0.182%, mid) (gnomAD).

What do computational predictors say about DOCK2 p.Met535Val (c.1603A>G)?

AlphaMissense predicts ambiguous (score 0.3994) — an in-silico prediction, not a clinical call.

DOCK2 p.Met535Val

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.1603A>G · rs143942535 · VCV747168

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.3994 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.182%, mid)

Conditions

DOCK2 deficiency

Computational evidence

Protein change
AlphaMissense	0.3994	ambiguous
REVEL	0.308	indeterminate
SaProt	LLR -9.58	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.2, phastCons 1
Regional constraint	o/e 0.72	unconstrained · MANE · 348 kb · p 3.1e-21 · regional, not allelic
Overall
CADD	24.8	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.182% Middle Eastern · 11/6,058 alleles

Filtering AF 0.102% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0787%

Overall 0.0239% 386/1,614,124 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.47%	213
Middle Easterngrpmax	0.182%	551
Remaining individualsnot grpmax-eligible	0.0576%	1,736
South Asian	0.0384%	2,603
Admixed American	0.0366%	2,729
European (non-Finnish)	0.0119%	8,368
African / African-American	0.00267%	37,523

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Met535Val
Coding: c.1603A>G
MANE Select: NM_004946
dbSNP: rs143942535
Type: single nucleotide variant
Location: chr5:169712167 (GRCh38)
Gene constraint: LOEUF 0.421 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 80.40 · 6 PDB
Residue 535: 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 p.Met535Thr 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-met535val (accessed [today's date]).

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