Is DSPP p.Asp1086Val (c.3257A>T) pathogenic?

DSPP p.Asp1086Val (c.3257A>T) is classified Uncertain significance in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-23). AlphaMissense: ambiguous (0.3568); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with DSPP p.Asp1086Val (c.3257A>T)?

DSPP p.Asp1086Val (c.3257A>T) is associated with Inborn genetic diseases (ClinVar).

How common is DSPP p.Asp1086Val (c.3257A>T) in the general population?

DSPP p.Asp1086Val (c.3257A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DSPP p.Asp1086Val (c.3257A>T)?

AlphaMissense predicts ambiguous (score 0.3568) — an in-silico prediction, not a clinical call.

DSPP p.Asp1086Val

c.3257A>T · rs2475886560 · VCV3086014

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3568 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3568	ambiguous
REVEL	0.248	benign-leaning
SaProt	LLR -13.51	damaging
⇒ SaProt calls this damaging; REVEL does not; AlphaMissense makes no call.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 2.2	GERP -1.6, phastCons 0.012
Regional constraint	o/e 0.38	unconstrained · MANE · 513 bp · p 9.7e-18 · regional, not allelic
Overall
CADD	16.15	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DSPP
Protein: p.Asp1086Val
Coding: c.3257A>T
MANE Select: NM_014208
dbSNP: rs2475886560
Type: single nucleotide variant
Location: chr4:87615919 (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-asp1086val (accessed [today's date]).

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