Is DSPP p.984DSS[4] (c.2952TAGCAGTGACAGCAGTGA[1]) pathogenic?

DSPP p.984DSS[4] (c.2952TAGCAGTGACAGCAGTGA[1]) is classified Benign in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2018-11-11). Common (popmax 6.62%, afr) — too common for a highly-penetrant pathogenic allele.

How common is DSPP p.984DSS[4] (c.2952TAGCAGTGACAGCAGTGA[1]) in the general population?

DSPP p.984DSS[4] (c.2952TAGCAGTGACAGCAGTGA[1]) is common (popmax 6.62%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

DSPP p.984DSS[4]

c.2952TAGCAGTGACAGCAGTGA[1] · rs752353583 · VCV1229557

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 6.62%, afr) — too common for a highly-penetrant pathogenic allele

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 -1.6
Overall
CADD	2.567	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 6.62% African / African-American · 4,570/69,022 alleles

Filtering AF 6.46% ClinGen BA1/BS1 input FAF95, joint · FAF99 6.4%

Overall 0.334% 5,153/1,544,816 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	6.62%	15
Admixed American	0.52%	192
Remaining individualsnot grpmax-eligible	0.437%	229
Middle Eastern	0.0503%	1,987
South Asian	0.0179%	5,581
European (non-Finnish)	0.0034%	29,383
East Asian	0.00245%	40,746

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.984DSS[4]
Coding: c.2952TAGCAGTGACAGCAGTGA[1]
dbSNP: rs752353583
Type: Microsatellite
Location: chr4:87615612 (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-984dss-4 (accessed [today's date]).

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