Is DCC p.Gly556fs (c.1667del) pathogenic?

DCC p.Gly556fs (c.1667del) is classified Likely pathogenic in DCC (ClinVar, Single submitter, 1 submitter; last evaluated 2018-11-19). Absent from gnomAD.

How common is DCC p.Gly556fs (c.1667del) in the general population?

DCC p.Gly556fs (c.1667del) is absent from gnomAD (gnomAD).

DCC p.Gly556fs

c.1667del · rs1568364038 · VCV599011

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

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 10 of 29
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.046	GERP -1.7, phastCons 0.89

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.Gly556fs
Coding: c.1667del
MANE Select: NM_005215
dbSNP: rs1568364038
Type: Deletion
Location: chr18:53205308 (GRCh38)
Gene constraint: LOEUF 0.414 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 68.60 · 9 PDB
Residue 556: the fibronectin type-iii 2 domain; a UniProt-annotated variant site (in mrmv1; likely pathogenic)

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

Similar variants

DCC p.Gly556Ser Uncertain significance ★ ⚠ same residue
DCC p.Asn678fs Likely pathogenic ★ same type
DCC p.Ile760fs Pathogenic ★ same type
DCC p.Lys419fs Likely pathogenic ★ same type
DCC p.Pro1315fs Pathogenic ★ same type
DCC p.Pro847fs Pathogenic ★ same type
DCC p.Val263fs Pathogenic ★ same type
DCC p.Val489fs 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/dcc-p-gly556fs (accessed [today's date]).

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