Is DSPP p.Asp1068= (c.3204T>C) pathogenic?

DSPP p.Asp1068= (c.3204T>C) is classified Benign/Likely benign in DSPP (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-12-01). Rare (popmax 0.662%, nfe).

How common is DSPP p.Asp1068= (c.3204T>C) in the general population?

DSPP p.Asp1068= (c.3204T>C) is rare (popmax 0.662%, nfe) (gnomAD).

DSPP p.Asp1068=

c.3204T>C · rs370264407 · VCV993972

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.662%, 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 -2.1
Overall
CADD	0.415	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.662% European (non-Finnish) · 7,303/1,102,802 alleles

Filtering AF 0.649% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.644%

Overall 0.661% 9,772/1,479,016 alleles · rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	2.45%	41
European (non-Finnish)grpmax	0.662%	151
Remaining individualsnot grpmax-eligible	0.661%	151
Admixed American	0.574%	174
Middle Eastern	0.319%	313
African / African-American	0.261%	384
South Asian	0.237%	423
Ashkenazi Jewishnot grpmax-eligible	0.203%	492
Amishnot grpmax-eligible	0.13%	768
East Asian	0.0495%	2,019

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Asp1068=
Coding: c.3204T>C
dbSNP: rs370264407
Type: single nucleotide variant
Location: chr4:87615866 (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-asp1068 (accessed [today's date]).

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