Is DSPP p.1152DSS[8] (c.3501CAGCAGCGA[1]) pathogenic?

DSPP p.1152DSS[8] (c.3501CAGCAGCGA[1]) is classified Likely benign in DSPP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-11-20). Low-frequency (popmax 1.21%, afr).

How common is DSPP p.1152DSS[8] (c.3501CAGCAGCGA[1]) in the general population?

DSPP p.1152DSS[8] (c.3501CAGCAGCGA[1]) is low-frequency (popmax 1.21%, afr) (gnomAD).

DSPP p.1152DSS[8]

c.3501CAGCAGCGA[1] · rs1351412719 · VCV1190904

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.21%, afr)

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 -2.3
Overall
CADD	2.248	PHRED · no single calibrated threshold — expert panels disagree
Region caveats
Repeat context	tandem	GATAGCAGT simple repeat · ambiguous alignment · confidence, not pathogenicity

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.21% African / African-American · 424/35,100 alleles

Filtering AF 1.11% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.08%

Overall 0.223% 1,644/737,890 alleles · low-frequency

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	1.68%	60
African / African-Americangrpmax	1.21%	83
Remaining individualsnot grpmax-eligible	0.397%	252
Admixed American	0.309%	324
Middle Eastern	0.185%	540
European (non-Finnish)	0.14%	713
South Asian	0.106%	946
Finnishnot grpmax-eligible	0.0344%	2,904
East Asian	0.0298%	3,358

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.1152DSS[8]
Coding: c.3501CAGCAGCGA[1]
dbSNP: rs1351412719
Type: Microsatellite
Location: chr4:87616155 (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-1152dss-8 (accessed [today's date]).

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