Is DSPP p.Asp990= (c.2970T>C) pathogenic?

DSPP p.Asp990= (c.2970T>C) is classified Likely benign in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2026-03-01). Ultra-rare (popmax 0.0128%, afr).

How common is DSPP p.Asp990= (c.2970T>C) in the general population?

DSPP p.Asp990= (c.2970T>C) is ultra-rare (popmax 0.0128%, afr) (gnomAD).

DSPP p.Asp990=

c.2970T>C · rs375979015 · VCV2654899

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0128%, 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 -16	GERP -1.8
Overall
CADD	0.17	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0128% African / African-American · 8/62,616 alleles

Filtering AF 0.00628% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00455%

Overall 0.00361% 55/1,523,504 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0128%	7,827
Finnishnot grpmax-eligible	0.0121%	8,293
East Asian	0.0101%	9,937
European (non-Finnish)	0.0029%	34,471
South Asian	0.00242%	41,287
Remaining individualsnot grpmax-eligible	0.00169%	59,000

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.Asp990=
Coding: c.2970T>C
dbSNP: rs375979015
Type: single nucleotide variant
Location: chr4:87615632 (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-asp990 (accessed [today's date]).

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