Is DSPP p.Ser1076= (c.3228C>T) pathogenic?

DSPP p.Ser1076= (c.3228C>T) is classified Likely benign in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2026-04-01). Ultra-rare (popmax 0.0664%, afr).

How common is DSPP p.Ser1076= (c.3228C>T) in the general population?

DSPP p.Ser1076= (c.3228C>T) is ultra-rare (popmax 0.0664%, afr) (gnomAD).

DSPP p.Ser1076=

c.3228C>T · VCV3387850

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0664%, 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 -2.1
Overall
CADD	0.65	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0664% African / African-American · 38/57,258 alleles

Filtering AF 0.0496% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0439%

Overall 0.00828% 125/1,510,502 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0664%	1,507
Finnishnot grpmax-eligible	0.0334%	2,990
Admixed American	0.0212%	4,709
South Asian	0.016%	6,236
East Asian	0.0128%	7,807
Remaining individualsnot grpmax-eligible	0.0102%	9,789
Ashkenazi Jewishnot grpmax-eligible	0.00707%	14,135
European (non-Finnish)	0.00282%	35,490

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.Ser1076=
Coding: c.3228C>T
Type: single nucleotide variant
Location: chr4:87615890 (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-ser1076 (accessed [today's date]).

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