Is DOCK7 p.Ser900= (c.2700C>T) pathogenic?

DOCK7 p.Ser900= (c.2700C>T) is classified Benign/Likely benign in DOCK7 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-12-22). Rare (popmax 0.481%, afr); Associated with developmental and epileptic encephalopathy, 23.

What condition is associated with DOCK7 p.Ser900= (c.2700C>T)?

DOCK7 p.Ser900= (c.2700C>T) is associated with developmental and epileptic encephalopathy, 23 (ClinVar).

How common is DOCK7 p.Ser900= (c.2700C>T) in the general population?

DOCK7 p.Ser900= (c.2700C>T) is rare (popmax 0.481%, afr) (gnomAD).

DOCK7 p.Ser900=

c.2700C>T · rs35648144 · VCV475134

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

rare (popmax 0.481%, afr)

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 1.3	GERP -3.1, phastCons 1
Overall
CADD	7.739	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.481% African / African-American · 361/75,022 alleles

Filtering AF 0.44% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.424%

Overall 0.0256% 413/1,613,954 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.481%	208
Admixed American	0.0433%	2,308
Middle Eastern	0.033%	3,031
Remaining individualsnot grpmax-eligible	0.0304%	3,290
South Asian	0.0022%	45,520
European (non-Finnish)	0.000254%	393,317

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.Ser900=
Coding: c.2700C>T
MANE Select: NM_001367561
dbSNP: rs35648144
Type: single nucleotide variant
Location: chr1:62552798 (GRCh38)
Gene constraint: LOEUF 0.551 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 74.60 · 2 PDB
Residue 900: a modified residue (phosphoserine); the 'disordered' region

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 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
DOCK7 p.Ala1479Thr 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-ser900 (accessed [today's date]).

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