Is DMP1 p.Ser397Cys (c.1189A>T) pathogenic?

DMP1 p.Ser397Cys (c.1189A>T) is classified Uncertain significance in DMP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-10). AlphaMissense: ambiguous (0.4636); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with DMP1 p.Ser397Cys (c.1189A>T)?

DMP1 p.Ser397Cys (c.1189A>T) is associated with Inborn genetic diseases (ClinVar).

How common is DMP1 p.Ser397Cys (c.1189A>T) in the general population?

DMP1 p.Ser397Cys (c.1189A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DMP1 p.Ser397Cys (c.1189A>T)?

AlphaMissense predicts ambiguous (score 0.4636) — an in-silico prediction, not a clinical call.

DMP1 p.Ser397Cys

c.1189A>T · VCV4241421

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4636 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.4636	ambiguous
REVEL	0.391	indeterminate
SaProt	LLR -11.97	damaging
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 7.1	GERP 1.8, phastCons 1
Overall
CADD	22.6	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: DMP1
Protein: p.Ser397Cys
Coding: c.1189A>T
Type: single nucleotide variant
Location: chr4:87662967 (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-ser397cys (accessed [today's date]).

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