Is DSPP p.Ser1151= (c.3453C>T) pathogenic?

DSPP p.Ser1151= (c.3453C>T) is classified Likely benign in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-01). Ultra-rare (popmax 0.0309%, afr).

How common is DSPP p.Ser1151= (c.3453C>T) in the general population?

DSPP p.Ser1151= (c.3453C>T) is ultra-rare (popmax 0.0309%, afr) (gnomAD).

DSPP p.Ser1151=

c.3453C>T · rs769550660 · VCV2654919

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0309%, 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 -1.7
Overall
CADD	3.999	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0309% African / African-American · 20/64,796 alleles

Filtering AF 0.0204% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.017%

Overall 0.00764% 115/1,504,880 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0309%	3,240
Admixed American	0.0192%	5,198
Middle Eastern	0.0177%	5,640
South Asian	0.0149%	6,706
Finnishnot grpmax-eligible	0.0143%	6,987
Ashkenazi Jewishnot grpmax-eligible	0.011%	9,127
Remaining individualsnot grpmax-eligible	0.0103%	9,680
East Asian	0.0102%	9,785
European (non-Finnish)	0.00462%	21,651

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.Ser1151=
Coding: c.3453C>T
dbSNP: rs769550660
Type: single nucleotide variant
Location: chr4:87616115 (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-ser1151 (accessed [today's date]).

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