Is DCC p.Asn678fs (c.2034_2038del) pathogenic?

DCC p.Asn678fs (c.20342038del) is classified Likely pathogenic in DCC (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-29). Absent from gnomAD.

How common is DCC p.Asn678fs (c.2034_2038del) in the general population?

DCC p.Asn678fs (c.2034_2038del) is absent from gnomAD (gnomAD).

DCC p.Asn678fs

c.2034_2038del · rs2511410848 · VCV1710471

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 13 of 29
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.3	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: DCC
Protein: p.Asn678fs
Coding: c.2034_2038del
MANE Select: NM_005215
dbSNP: rs2511410848
Type: Deletion
Location: chr18:53305700 (GRCh38)
Gene constraint: LOEUF 0.414 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 68.60 · 9 PDB
Residue 678: the fibronectin type-iii 3 domain; a UniProt-annotated variant site (in mrmv1; likely pathogenic)

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

Disease context

— disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DCC p.Ile760fs Pathogenic ★ same condition
DCC p.Lys419fs Likely pathogenic ★ same condition
DCC p.Val263fs Pathogenic ★ same condition
DCC p.Val793fs Pathogenic ★ same condition
DCC p.Asn678Ser Likely benign ★ same residue
DCC p.Asp233_Leu328del Pathogenic same condition
DCC p.Thr309fs Pathogenic same condition
DCC p.Arg1025Ter Pathogenic/Likely pathogenic ★★ 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/dcc-p-asn678fs (accessed [today's date]).

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