Is DSPP p.Ser1007fs (c.3019del) pathogenic?

DSPP p.Ser1007fs (c.3019del) is classified Pathogenic/Likely pathogenic in DSPP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-03-04). Associated with DSPP-related disorders.

What condition is associated with DSPP p.Ser1007fs (c.3019del)?

DSPP p.Ser1007fs (c.3019del) is associated with DSPP-related disorders (ClinVar).

DSPP p.Ser1007fs

c.3019del · VCV3765381

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

DSPP-related disorders

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -20	GERP -1.7
Region caveats
Repeat context	tandem	MLT1N2 ltr, simple repeat · ambiguous alignment · confidence, not pathogenicity

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

Variant & gene context

Gene: DSPP
Protein: p.Ser1007fs
Coding: c.3019del
Type: Deletion
Location: chr4:87615681 (GRCh38)

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

Disease context

DSPP-related disorders

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/dspp-p-ser1007fs (accessed [today's date]).

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