Is DOCK2 p.Arg572= (c.1716A>T) pathogenic?

DOCK2 p.Arg572= (c.1716A>T) is classified Likely benign in DOCK2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-04-01). Very rare (popmax 0.0088%, sas); Associated with DOCK2-related disorder.

What condition is associated with DOCK2 p.Arg572= (c.1716A>T)?

DOCK2 p.Arg572= (c.1716A>T) is associated with DOCK2-related disorder (ClinVar).

How common is DOCK2 p.Arg572= (c.1716A>T) in the general population?

DOCK2 p.Arg572= (c.1716A>T) is very rare (popmax 0.0088%, sas) (gnomAD).

DOCK2 p.Arg572=

c.1716A>T · rs760775098 · VCV3057400

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0088%, sas)

Conditions

DOCK2-related disorder

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 0.034	GERP -4.8, phastCons 0.013
Overall
CADD	7.993	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0088% South Asian · 8/90,958 alleles

Filtering AF 0.00437% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00312%

Overall 0.000547% 8/1,461,328 alleles · very rare

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.Arg572=
Coding: c.1716A>T
MANE Select: NM_004946
dbSNP: rs760775098
Type: single nucleotide variant
Location: chr5:169714084 (GRCh38)
Gene constraint: LOEUF 0.421 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 80.40 · 6 PDB
Residue 572: the c2 dock-type domain

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

Disease context

DOCK2-related disorder

Similar variants

DOCK2 p.Met120Ile Uncertain significance ★★ ⚠ same condition
DOCK2 p.Lys286Ter Likely pathogenic ★ same condition
DOCK2 p.Thr1809Ala Conflicting classifications of pathogenicity ★ ⚠ same condition
DOCK2 c.169-11_169-7del Likely benign same condition
DOCK2 c.2267+3G>A Uncertain significance ★★ same type
DOCK2 c.2704-3C>T Uncertain significance ★★ same type
DOCK2 c.4467+4A>G Uncertain significance ★★ same type
DOCK2 p.Ala1393Val Uncertain significance ★★ ⚠ same type

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-arg572 (accessed [today's date]).

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