Is DSPP p.Asp1041Glu (c.3123T>G) pathogenic?

DSPP p.Asp1041Glu (c.3123T>G) is classified Uncertain significance in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2021-11-29). AlphaMissense: likely benign (0.2484); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with DSPP p.Asp1041Glu (c.3123T>G)?

DSPP p.Asp1041Glu (c.3123T>G) is associated with Inborn genetic diseases (ClinVar).

How common is DSPP p.Asp1041Glu (c.3123T>G) in the general population?

DSPP p.Asp1041Glu (c.3123T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DSPP p.Asp1041Glu (c.3123T>G)?

AlphaMissense predicts likely benign (score 0.2484) — an in-silico prediction, not a clinical call.

DSPP p.Asp1041Glu

c.3123T>G · rs1342008580 · VCV2262335

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2484 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2484	likely benign
REVEL	0.248	benign-leaning
SaProt	LLR -10.28	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -20	GERP -1.7
Regional constraint	o/e 0.38	unconstrained · MANE · 513 bp · p 9.7e-18 · regional, not allelic
Overall
CADD	0.432	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.Asp1041Glu
Coding: c.3123T>G
dbSNP: rs1342008580
Type: single nucleotide variant
Location: chr4:87615785 (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-asp1041glu (accessed [today's date]).

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