Is DOCK7 p.Val290= (c.870C>T) pathogenic?

DOCK7 p.Val290= (c.870C>T) is classified Likely benign in DOCK7 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-02-03). Very rare (popmax 0.00512%, amr); Associated with developmental and epileptic encephalopathy, 23.

What condition is associated with DOCK7 p.Val290= (c.870C>T)?

DOCK7 p.Val290= (c.870C>T) is associated with developmental and epileptic encephalopathy, 23 (ClinVar).

How common is DOCK7 p.Val290= (c.870C>T) in the general population?

DOCK7 p.Val290= (c.870C>T) is very rare (popmax 0.00512%, amr) (gnomAD).

DOCK7 p.Val290=

c.870C>T · rs1405369707 · VCV1568394

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00512%, amr)

Conditions

developmental and epileptic encephalopathy, 23

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 1.2	GERP -1.6, phastCons 1
Overall
CADD	7.597	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00512% Admixed American · 3/58,606 alleles

Filtering AF 0.00136% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000677%

Overall 0.000375% 6/1,598,466 alleles · very rare exomes 6/1,446,474 · genomes 0/151,992 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00512%	19,535
South Asian	0.0034%	29,373

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.Val290=
Coding: c.870C>T
MANE Select: NM_001367561
dbSNP: rs1405369707
Type: single nucleotide variant
Location: chr1:62636552 (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.Val290Ala Uncertain significance ★★ ⚠ same residue
DOCK7 p.Val290Ile Uncertain significance ★★ ⚠ 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

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-val290 (accessed [today's date]).

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