Is DSPP p.1005DSS[3] (c.3024CAGCAGTGA[1]) pathogenic?

DSPP p.1005DSS[3] (c.3024CAGCAGTGA[1]) is classified Conflicting classifications of pathogenicity in DSPP (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2026-03-01). Rare (popmax 0.696%, nfe).

How common is DSPP p.1005DSS[3] (c.3024CAGCAGTGA[1]) in the general population?

DSPP p.1005DSS[3] (c.3024CAGCAGTGA[1]) is rare (popmax 0.696%, nfe) (gnomAD).

DSPP p.1005DSS[3]

c.3024CAGCAGTGA[1] · rs762157486 · VCV445476

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

rare (popmax 0.696%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -20	GERP -1.7
Overall
CADD	5.218	PHRED · no single calibrated threshold — expert panels disagree
Region caveats
Repeat context	tandem	MLT1N2 ltr, simple repeat · ambiguous alignment · confidence, not pathogenicity

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.696% European (non-Finnish) · 7,898/1,134,288 alleles

Filtering AF 0.683% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.678%

Overall 0.585% 8,889/1,520,544 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.696%	144
Remaining individualsnot grpmax-eligible	0.447%	224
South Asian	0.437%	229
East Asian	0.243%	412
Admixed American	0.222%	451
Finnishnot grpmax-eligible	0.148%	678
African / African-American	0.111%	903
Middle Eastern	0.052%	1,924
Ashkenazi Jewishnot grpmax-eligible	0.0286%	3,498

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: DSPP
Protein: p.1005DSS[3]
Coding: c.3024CAGCAGTGA[1]
dbSNP: rs762157486
Type: Microsatellite
Location: chr4:87615678 (GRCh38)

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

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-1005dss-3 (accessed [today's date]).

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