Is DSPP p.Asp1035Asn (c.3103G>A) pathogenic?

DSPP p.Asp1035Asn (c.3103G>A) is classified Likely benign in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-16). AlphaMissense: likely benign (0.104); Very rare (popmax 0.00623%, amr).

How common is DSPP p.Asp1035Asn (c.3103G>A) in the general population?

DSPP p.Asp1035Asn (c.3103G>A) is very rare (popmax 0.00623%, amr) (gnomAD).

What do computational predictors say about DSPP p.Asp1035Asn (c.3103G>A)?

AlphaMissense predicts likely benign (score 0.104) — an in-silico prediction, not a clinical call.

DSPP p.Asp1035Asn

c.3103G>A · VCV3910405

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.104 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00623%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.104	likely benign
REVEL	0.123	moderately benign-leaning
SaProt	LLR -8.55	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -2.1	GERP -1.2
Regional constraint	o/e 0.38	unconstrained · MANE · 513 bp · p 9.7e-18 · regional, not allelic
Overall
CADD	7.285	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 0.00623% Admixed American · 2/32,078 alleles

Filtering AF 0.00273% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00233%

Overall 0.00392% 29/739,396 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00623%	16,039
South Asian	0.00563%	17,751
East Asian	0.00439%	22,756
European (non-Finnish)	0.00417%	23,980
Remaining individualsnot grpmax-eligible	0.00339%	29,456
African / African-American	0.00231%	43,260

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.Asp1035Asn
Coding: c.3103G>A
Type: single nucleotide variant
Location: chr4:87615765 (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-asp1035asn (accessed [today's date]).

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