Is DSPP p.Ser1193= (c.3579C>T) pathogenic?

DSPP p.Ser1193= (c.3579C>T) is classified Likely benign in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-01). Rare (popmax 0.14%, afr).

How common is DSPP p.Ser1193= (c.3579C>T) in the general population?

DSPP p.Ser1193= (c.3579C>T) is rare (popmax 0.14%, afr) (gnomAD).

DSPP p.Ser1193=

c.3579C>T · rs372841521 · VCV2654928

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.14%, 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 -2.7
Overall
CADD	0.235	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.14% African / African-American · 85/60,542 alleles

Filtering AF 0.116% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.107%

Overall 0.00929% 138/1,485,600 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.14%	712
Admixed American	0.0349%	2,867
Remaining individualsnot grpmax-eligible	0.0296%	3,383
Middle Eastern	0.0177%	5,648
South Asian	0.00623%	16,044
East Asian	0.00264%	37,910
European (non-Finnish)	0.00117%	85,720

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.Ser1193=
Coding: c.3579C>T
dbSNP: rs372841521
Type: single nucleotide variant
Location: chr4:87616241 (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-ser1193 (accessed [today's date]).

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