Is DSPP p.984DSS[9] (c.2976_3002dup) pathogenic?

DSPP p.984DSS[9] (c.29763002dup) is classified Likely benign in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2019-10-29). Low-frequency (popmax 1.72%, afr).

How common is DSPP p.984DSS[9] (c.2976_3002dup) in the general population?

DSPP p.984DSS[9] (c.2976_3002dup) is low-frequency (popmax 1.72%, afr) (gnomAD).

DSPP p.984DSS[9]

c.2976_3002dup · rs755728099 · VCV1202482

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 1.72%, 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 -1.8
Overall
CADD	1.456	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 1.72% African / African-American · 1,032/60,072 alleles

Filtering AF 1.63% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.6%

Overall 0.0767% 1,176/1,532,248 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.72%	58
Admixed American	0.136%	733
Remaining individualsnot grpmax-eligible	0.0894%	1,119
Middle Eastern	0.0169%	5,914
South Asian	0.00359%	27,853
European (non-Finnish)	0.00166%	60,239

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[9]
Coding: c.2976_3002dup
dbSNP: rs755728099
Type: Duplication
Location: chr4:87615614 (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-9 (accessed [today's date]).

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