Is DSPP p.Ser1103= (c.3309C>T) pathogenic?

DSPP p.Ser1103= (c.3309C>T) is classified Benign in DSPP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-11-10). Common (popmax 41.7%, eas) — too common for a highly-penetrant pathogenic allele.

DSPP p.Ser1103=

Q: How common is DSPP p.Ser1103= (c.3309C>T) in the general population?

DSPP p.Ser1103= (c.3309C>T) is common (popmax 41.7%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.3309C>T · rs372453629 · VCV1282039

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 41.7%, eas) — 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 -2.1
Overall
CADD	1.305	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 41.7% East Asian · 2,439/5,848 alleles

Filtering AF 40.3% ClinGen BA1/BS1 input FAF95, joint · FAF99 39.8%

Overall 12.4% 38,934/313,818 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	41.7%	2
Finnishnot grpmax-eligible	41.5%	2
Admixed American	26.9%	4
African / African-American	21.2%	5
Remaining individualsnot grpmax-eligible	16.7%	6
European (non-Finnish)	10.4%	10
Middle Eastern	9.95%	10
Ashkenazi Jewishnot grpmax-eligible	9.89%	10
Amishnot grpmax-eligible	6.43%	16
South Asian	5.7%	18

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.Ser1103=
Coding: c.3309C>T
dbSNP: rs372453629
Type: single nucleotide variant
Location: chr4:87615971 (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-ser1103 (accessed [today's date]).

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