Is DOCK7 p.Pro1684fs (c.5049del) pathogenic?

DOCK7 p.Pro1684fs (c.5049del) is classified Pathogenic in DOCK7 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-01). Absent from gnomAD.

How common is DOCK7 p.Pro1684fs (c.5049del) in the general population?

DOCK7 p.Pro1684fs (c.5049del) is absent from gnomAD (gnomAD).

DOCK7 p.Pro1684fs

c.5049del · rs1064797112 · VCV424899

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 40 of 50
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 2.8, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DOCK7
Protein: p.Pro1684fs
Coding: c.5049del
MANE Select: NM_001367561
dbSNP: rs1064797112
Type: Deletion
Location: chr1:62494443 (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 1684: the docker domain

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

Similar variants

DOCK7 p.Pro1684= Likely benign ★ same residue
DOCK7 p.Phe1206fs Pathogenic/Likely pathogenic ★★ same type
DOCK7 p.Met1284del Uncertain significance ★★ same type
DOCK7 c.1283-14del Benign/Likely benign ★★ same type
DOCK7 c.1683-51_1683-50del Benign ★★ same type
DOCK7 c.1872-9del Benign/Likely benign ★★ same type
DOCK7 c.2113-38del Benign ★★ same type
DOCK7 c.3781+15_3781+56del Benign/Likely benign ★★ 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-pro1684fs (accessed [today's date]).

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