Is DSPP p.Asn1029Asp (c.3085A>G) pathogenic?

DSPP p.Asn1029Asp (c.3085A>G) is classified Likely benign in DSPP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-11-10). AlphaMissense: likely benign (0.0632); Low-frequency (popmax 2.92%, eas).

How common is DSPP p.Asn1029Asp (c.3085A>G) in the general population?

DSPP p.Asn1029Asp (c.3085A>G) is low-frequency (popmax 2.92%, eas) (gnomAD).

What do computational predictors say about DSPP p.Asn1029Asp (c.3085A>G)?

AlphaMissense predicts likely benign (score 0.0632) — an in-silico prediction, not a clinical call.

DSPP p.Asn1029Asp

c.3085A>G · rs150637282 · VCV1208931

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0632 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.92%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0632	likely benign
REVEL	0.209	benign-leaning
SaProt	LLR -5.51	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -3.4	GERP -1.3
Regional constraint	o/e 0.38	unconstrained · MANE · 513 bp · p 9.7e-18 · regional, not allelic
Overall
CADD	0.137	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.92% East Asian · 449/15,360 alleles

Filtering AF 2.7% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.61%

Overall 1.77% 5,311/299,320 alleles · low-frequency

Ancestry group	Frequency	1 in
East Asiangrpmax	2.92%	34
South Asian	2.59%	39
Finnishnot grpmax-eligible	2.24%	45
Remaining individualsnot grpmax-eligible	1.82%	55
European (non-Finnish)	1.79%	56
Middle Eastern	1.5%	67
Ashkenazi Jewishnot grpmax-eligible	1.16%	86
Admixed American	1.13%	89
African / African-American	0.582%	172

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.Asn1029Asp
Coding: c.3085A>G
dbSNP: rs150637282
Type: single nucleotide variant
Location: chr4:87615747 (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-asn1029asp (accessed [today's date]).

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