Is DSPP p.Asn1179Asp (c.3535A>G) pathogenic?

DSPP p.Asn1179Asp (c.3535A>G) is classified Likely benign in DSPP (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-03-01). AlphaMissense: likely benign (0.057); Rare (popmax 0.787%, afr).

How common is DSPP p.Asn1179Asp (c.3535A>G) in the general population?

DSPP p.Asn1179Asp (c.3535A>G) is rare (popmax 0.787%, afr) (gnomAD).

What do computational predictors say about DSPP p.Asn1179Asp (c.3535A>G)?

AlphaMissense predicts likely benign (score 0.057) — an in-silico prediction, not a clinical call.

DSPP p.Asn1179Asp

c.3535A>G · rs201659235 · VCV1205890

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.057 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.787%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.057	likely benign
REVEL	0.155	moderately benign-leaning
SaProt	LLR -4.18	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -5	GERP -3
Regional constraint	o/e 0.72	unconstrained · MANE · 391 bp · p 0.00018 · regional, not allelic
Overall
CADD	0.382	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 0.787% African / African-American · 426/54,098 alleles

Filtering AF 0.726% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.701%

Overall 0.105% 1,487/1,419,682 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.787%	127
East Asian	0.504%	198
Ashkenazi Jewishnot grpmax-eligible	0.468%	214
Middle Eastern	0.396%	253
Admixed American	0.199%	502
Remaining individualsnot grpmax-eligible	0.186%	539
South Asian	0.119%	841
European (non-Finnish)	0.044%	2,272
Finnishnot grpmax-eligible	0.0155%	6,450

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.Asn1179Asp
Coding: c.3535A>G
dbSNP: rs201659235
Type: single nucleotide variant
Location: chr4:87616197 (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-asn1179asp (accessed [today's date]).

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