Is DSPP p.Ser1130= (c.3390C>T) pathogenic?

DSPP p.Ser1130= (c.3390C>T) is classified Benign/Likely benign in DSPP (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-11-26). Rare (popmax 0.112%, eas).

How common is DSPP p.Ser1130= (c.3390C>T) in the general population?

DSPP p.Ser1130= (c.3390C>T) is rare (popmax 0.112%, eas) (gnomAD).

DSPP p.Ser1130=

c.3390C>T · rs536124533 · VCV1280005

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.112%, eas)

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 -7.4	GERP -2.3
Overall
CADD	1.363	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.112% East Asian · 4/3,570 alleles

Filtering AF 0.0395% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0312%

Overall 0.0504% 55/109,188 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.112%	892
South Asian	0.0705%	1,418
African / African-American	0.0622%	1,609
European (non-Finnish)	0.0482%	2,075
Remaining individualsnot grpmax-eligible	0.0448%	2,230
Admixed American	0.0436%	2,296

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.Ser1130=
Coding: c.3390C>T
dbSNP: rs536124533
Type: single nucleotide variant
Location: chr4:87616052 (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-ser1130 (accessed [today's date]).

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