Is DMP1 p.Ser299Arg (c.895A>C) pathogenic?

DMP1 p.Ser299Arg (c.895A>C) is classified Uncertain significance in DMP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-21). AlphaMissense: likely benign (0.176); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with DMP1 p.Ser299Arg (c.895A>C)?

DMP1 p.Ser299Arg (c.895A>C) is associated with Inborn genetic diseases (ClinVar).

How common is DMP1 p.Ser299Arg (c.895A>C) in the general population?

DMP1 p.Ser299Arg (c.895A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DMP1 p.Ser299Arg (c.895A>C)?

AlphaMissense predicts likely benign (score 0.176) — an in-silico prediction, not a clinical call.

DMP1 p.Ser299Arg

c.895A>C · VCV4241418

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.176 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.176	likely benign
REVEL	0.035	moderately benign-leaning
SaProt	LLR -9.68	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.7	GERP -3.4
Overall
CADD	0.145	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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: DMP1
Protein: p.Ser299Arg
Coding: c.895A>C
Type: single nucleotide variant
Location: chr4:87662673 (GRCh38)

Full DMP1 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/dmp1-p-ser299arg (accessed [today's date]).

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