Is DSPP p.Asp1005= (c.3015T>C) pathogenic?

DSPP p.Asp1005= (c.3015T>C) is classified Likely benign in DSPP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-07-01). Ultra-rare (popmax 0.0513%, amr).

How common is DSPP p.Asp1005= (c.3015T>C) in the general population?

DSPP p.Asp1005= (c.3015T>C) is ultra-rare (popmax 0.0513%, amr) (gnomAD).

DSPP p.Asp1005=

c.3015T>C · VCV3388066

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0513%, amr)

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	0.107	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0513% Admixed American · 25/48,688 alleles

Filtering AF 0.0357% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0304%

Overall 0.00914% 139/1,520,406 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0513%	1,948
East Asian	0.0179%	5,589
Middle Eastern	0.0173%	5,772
Remaining individualsnot grpmax-eligible	0.0153%	6,536
South Asian	0.00982%	10,181
African / African-American	0.00759%	13,171
European (non-Finnish)	0.00723%	13,832
Ashkenazi Jewishnot grpmax-eligible	0.00357%	27,982
Finnishnot grpmax-eligible	0.00174%	57,592

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.Asp1005=
Coding: c.3015T>C
Type: single nucleotide variant
Location: chr4:87615677 (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-asp1005 (accessed [today's date]).

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