Is DOCK7 p.Leu564Pro (c.1691T>C) pathogenic?

DOCK7 p.Leu564Pro (c.1691T>C) is classified Uncertain significance in DOCK7 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-04-12). AlphaMissense: likely pathogenic (0.9967); Absent from gnomAD v4.1; Associated with DOCK7-related disorder.

What condition is associated with DOCK7 p.Leu564Pro (c.1691T>C)?

DOCK7 p.Leu564Pro (c.1691T>C) is associated with DOCK7-related disorder (ClinVar).

How common is DOCK7 p.Leu564Pro (c.1691T>C) in the general population?

DOCK7 p.Leu564Pro (c.1691T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DOCK7 p.Leu564Pro (c.1691T>C)?

AlphaMissense predicts likely pathogenic (score 0.9967) — an in-silico prediction, not a clinical call.

DOCK7 p.Leu564Pro

c.1691T>C · VCV3349741

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9967 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

DOCK7-related disorder

Computational evidence

Protein change
AlphaMissense	0.9967	likely pathogenic · top 4% in DOCK7
REVEL	0.716	pathogenic-leaning
SaProt	LLR -18.97	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.5, phastCons 1
Regional constraint	o/e 0.85	unconstrained · MANE · 175 kb · p 3.6e-10 · regional, not allelic
Overall
CADD	27.6	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DOCK7
Protein: p.Leu564Pro
Coding: c.1691T>C
MANE Select: NM_001367561
Type: single nucleotide variant
Location: chr1:62586616 (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 564: the c2 dock-type domain

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

Disease context

DOCK7-related disorder

Similar variants

DOCK7 p.Leu564Phe Uncertain significance ★★ same residue
DOCK7 c.38+2T>A Likely pathogenic ★ same condition
DOCK7 p.Arg1123Ter Likely pathogenic ★ same condition
DOCK7 c.1801-1544A>T Likely benign same condition
DOCK7 p.Gly2027fs Likely pathogenic ★ same condition
DOCK7 p.Met1925fs Likely pathogenic ★ same condition
DOCK7 p.Val1510fs Likely pathogenic same condition
DOCK7 c.4924-1G>A Pathogenic/Likely pathogenic ★★ 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/dock7-p-leu564pro (accessed [today's date]).

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