Is DSPP p.Ser983= (c.2949C>T) pathogenic?

DSPP p.Ser983= (c.2949C>T) is classified Likely benign in DSPP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-10-01). Very rare (popmax 0.00951%, nfe).

How common is DSPP p.Ser983= (c.2949C>T) in the general population?

DSPP p.Ser983= (c.2949C>T) is very rare (popmax 0.00951%, nfe) (gnomAD).

DSPP p.Ser983=

c.2949C>T · VCV3387908

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00951%, nfe)

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 -1.6
Overall
CADD	1.214	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00951% European (non-Finnish) · 109/1,145,922 alleles

Filtering AF 0.00806% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00749%

Overall 0.00764% 118/1,544,818 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00951%	10,513
South Asian	0.00478%	20,928
African / African-American	0.0029%	34,520
East Asian	0.00245%	40,746
Admixed American	0.00198%	50,574
Remaining individualsnot grpmax-eligible	0.00167%	59,954

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.Ser983=
Coding: c.2949C>T
Type: single nucleotide variant
Location: chr4:87615611 (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-ser983 (accessed [today's date]).

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