Is DSPP p.766DSS[3] (c.2292CAGTGACAGCAGTGATAG[1]) pathogenic?

DSPP p.766DSS[3] (c.2292CAGTGACAGCAGTGATAG[1]) is classified Uncertain significance in DSPP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-09-16). Ultra-rare (popmax 0.0339%, mid).

How common is DSPP p.766DSS[3] (c.2292CAGTGACAGCAGTGATAG[1]) in the general population?

DSPP p.766DSS[3] (c.2292CAGTGACAGCAGTGATAG[1]) is ultra-rare (popmax 0.0339%, mid) (gnomAD).

DSPP p.766DSS[3]

c.2292CAGTGACAGCAGTGATAG[1] · rs1270564167 · VCV2441039

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0339%, mid)

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 -12	GERP -1.4
Overall
CADD	1.028	PHRED · no single calibrated threshold — expert panels disagree
Region caveats
Repeat context	tandem	(CAGTGA)n simple repeat · ambiguous alignment · confidence, not pathogenicity

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0339% Middle Eastern · 2/5,906 alleles

Filtering AF 0.00596% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00247%

Overall 0.00208% 32/1,535,906 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0339%	2,953
Admixed American	0.00399%	25,087
Ashkenazi Jewishnot grpmax-eligible	0.00349%	28,628
European (non-Finnish)	0.00218%	45,843
Finnishnot grpmax-eligible	0.00168%	59,358
African / African-American	0.00164%	61,010

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.766DSS[3]
Coding: c.2292CAGTGACAGCAGTGATAG[1]
dbSNP: rs1270564167
Type: Microsatellite
Location: chr4:87614952 (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-766dss-3 (accessed [today's date]).

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