Is DMP1 p.Ile267Met (c.801T>G) pathogenic?

DMP1 p.Ile267Met (c.801T>G) is classified Uncertain significance in DMP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-07). AlphaMissense: likely benign (0.0937); Very rare (popmax 0.00134%, afr); Associated with Inborn genetic diseases.

What condition is associated with DMP1 p.Ile267Met (c.801T>G)?

DMP1 p.Ile267Met (c.801T>G) is associated with Inborn genetic diseases (ClinVar).

How common is DMP1 p.Ile267Met (c.801T>G) in the general population?

DMP1 p.Ile267Met (c.801T>G) is very rare (popmax 0.00134%, afr) (gnomAD).

What do computational predictors say about DMP1 p.Ile267Met (c.801T>G)?

AlphaMissense predicts likely benign (score 0.0937) — an in-silico prediction, not a clinical call.

DMP1 p.Ile267Met

c.801T>G · VCV3840504

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0937 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0937	likely benign
REVEL	0.011	strongly benign-leaning
SaProt	LLR -7.29	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.11	GERP -3.3
Overall
CADD	0.216	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

Grpmax group 0.00134% African / African-American · 1/74,844 alleles

Overall 0.000658% 1/151,970 alleles · very rare

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: DMP1
Protein: p.Ile267Met
Coding: c.801T>G
MANE Select: NM_001142327 · reported on NM_004407
Type: single nucleotide variant
Location: chr4:87662579 (GRCh38)
Structure: AlphaFold pLDDT 53.56 · 1 PDB
Residue 267: the 'required for dna-binding' region; the 'interaction with ccnd1, ccnd2 and ccnd3' region

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

Similar variants

DMP1 p.Arg302Ile Uncertain significance ★★ ⚠ same condition
DMP1 p.Asn233Lys Uncertain significance ★★ ⚠ same condition
DMP1 p.Asp453Asn Uncertain significance ★★ ⚠ same condition
DMP1 p.Glu385Lys Uncertain significance ★★ ⚠ same condition
DMP1 p.Glu398Gly Uncertain significance ★★ ⚠ same condition
DMP1 p.Glu470Lys Uncertain significance ★★ ⚠ same condition
DMP1 p.Gly207Ser Uncertain significance ★★ ⚠ same condition
DMP1 p.Gly512Cys Uncertain significance ★★ ⚠ same condition

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-ile267met (accessed [today's date]).

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