Is DSPP p.Asn1017Asp (c.3049A>G) pathogenic?

DSPP p.Asn1017Asp (c.3049A>G) is classified Likely benign in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-16). AlphaMissense: likely benign (0.0786); Ultra-rare (popmax 0.0338%, afr); Associated with Inborn genetic diseases.

What condition is associated with DSPP p.Asn1017Asp (c.3049A>G)?

DSPP p.Asn1017Asp (c.3049A>G) is associated with Inborn genetic diseases (ClinVar).

How common is DSPP p.Asn1017Asp (c.3049A>G) in the general population?

DSPP p.Asn1017Asp (c.3049A>G) is ultra-rare (popmax 0.0338%, afr) (gnomAD).

What do computational predictors say about DSPP p.Asn1017Asp (c.3049A>G)?

AlphaMissense predicts likely benign (score 0.0786) — an in-silico prediction, not a clinical call.

DSPP p.Asn1017Asp

c.3049A>G · VCV4015131

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0786 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0338%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0786	likely benign
REVEL	0.148	moderately benign-leaning
SaProt	LLR -5.68	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -3.3	GERP -1.7
Regional constraint	o/e 0.38	unconstrained · MANE · 513 bp · p 9.7e-18 · regional, not allelic
Overall
CADD	0.003	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 0.0338% African / African-American · 18/53,290 alleles

Filtering AF 0.0218% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.018%

Overall 0.0044% 61/1,386,022 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0338%	2,961
South Asian	0.0187%	5,351
Admixed American	0.0111%	9,003
Ashkenazi Jewishnot grpmax-eligible	0.00797%	12,549
Finnishnot grpmax-eligible	0.00633%	15,803
European (non-Finnish)	0.00188%	53,062
Remaining individualsnot grpmax-eligible	0.00184%	54,364

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.Asn1017Asp
Coding: c.3049A>G
Type: single nucleotide variant
Location: chr4:87615711 (GRCh38)

Full DSPP gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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-asn1017asp (accessed [today's date]).

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