Is DSPP p.Asp1080= (c.3240T>C) pathogenic?

DSPP p.Asp1080= (c.3240T>C) is classified Benign in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-01). Rare (popmax 0.869%, amr).

How common is DSPP p.Asp1080= (c.3240T>C) in the general population?

DSPP p.Asp1080= (c.3240T>C) is rare (popmax 0.869%, amr) (gnomAD).

DSPP p.Asp1080=

c.3240T>C · rs770176700 · VCV2654905

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.869%, amr)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

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
Overall
CADD	0.272	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.869% Admixed American · 214/24,622 alleles

Filtering AF 0.774% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.737%

Overall 0.443% 3,335/752,424 alleles · rare exomes 2,935/712,666 · genomes 400/39,758 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.869%	115
Amishnot grpmax-eligible	0.833%	120
South Asian	0.585%	171
East Asian	0.472%	212
Remaining individualsnot grpmax-eligible	0.444%	225
European (non-Finnish)	0.426%	235
Finnishnot grpmax-eligible	0.367%	272
African / African-American	0.324%	308
Ashkenazi Jewishnot grpmax-eligible	0.238%	419
Middle Eastern	0.236%	424

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.Asp1080=
Coding: c.3240T>C
MANE Select: NM_014208
dbSNP: rs770176700
Type: single nucleotide variant
Location: chr4:87615902 (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-asp1080 (accessed [today's date]).

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