Is DOCK7 p.Arg1462= (c.4386A>G) pathogenic?

DOCK7 p.Arg1462= (c.4386A>G) is classified Likely benign in DOCK7 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-31). Very rare (popmax 0.00224%, eas); Associated with developmental and epileptic encephalopathy, 23.

What condition is associated with DOCK7 p.Arg1462= (c.4386A>G)?

DOCK7 p.Arg1462= (c.4386A>G) is associated with developmental and epileptic encephalopathy, 23 (ClinVar).

How common is DOCK7 p.Arg1462= (c.4386A>G) in the general population?

DOCK7 p.Arg1462= (c.4386A>G) is very rare (popmax 0.00224%, eas) (gnomAD).

DOCK7 p.Arg1462=

c.4386A>G · rs540943948 · VCV2790900

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00224%, eas)

Conditions

developmental and epileptic encephalopathy, 23

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.1	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.4	GERP -2.1, phastCons 1
Overall
CADD	12.74	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00224% East Asian · 1/44,590 alleles

Overall 0.000187% 3/1,605,722 alleles · very rare exomes 2/1,453,388 · genomes 1/152,334 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00224%	44,590
Remaining individualsnot grpmax-eligible	0.00161%	62,176
European (non-Finnish)	8.49e-05%	1,177,930

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: DOCK7
Protein: p.Arg1462=
Coding: c.4386A>G
MANE Select: NM_001367561
dbSNP: rs540943948
Type: single nucleotide variant
Location: chr1:62508052 (GRCh38)
Gene constraint: LOEUF 0.551 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 74.60 · 2 PDB

Full DOCK7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

developmental and epileptic encephalopathy, 23 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DOCK7 p.Arg1462Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
DOCK7 c.4924-1G>A Pathogenic/Likely pathogenic ★★ same condition
DOCK7 p.Arg1380Ter Pathogenic ★★ same condition
DOCK7 p.Arg1415Ter Pathogenic/Likely pathogenic ★★ same condition
DOCK7 p.Arg429Ter Pathogenic/Likely pathogenic ★★ same condition
DOCK7 p.Arg445Ter Pathogenic/Likely pathogenic ★★ same condition
DOCK7 c.3781+4C>G Uncertain significance ★★ same condition
DOCK7 c.38+6T>C 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/dock7-p-arg1462 (accessed [today's date]).

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