Is DMP1 p.Trp33Ter (c.98G>A) pathogenic?

DMP1 p.Trp33Ter (c.98G>A) is classified Pathogenic in DMP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-31). Very rare (popmax 0.00225%, eas).

How common is DMP1 p.Trp33Ter (c.98G>A) in the general population?

DMP1 p.Trp33Ter (c.98G>A) is very rare (popmax 0.00225%, eas) (gnomAD).

DMP1 p.Trp33Ter

c.98G>A · rs766601503 · VCV595958

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00225%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.8	GERP -0.23, phastCons 1
Overall
CADD	36.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00225% East Asian · 1/44,436 alleles

Filtering AF 0.000936% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000765%

Overall 0.00124% 19/1,532,630 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00225%	44,436
European (non-Finnish)	0.00154%	65,100
African / African-American	0.00136%	73,418

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.Trp33Ter
Coding: c.98G>A
MANE Select: NM_001142327 · reported on NM_004407
dbSNP: rs766601503
Type: single nucleotide variant
Location: chr4:87657075 (GRCh38)
Structure: AlphaFold pLDDT 53.56 · 1 PDB
Residue 33: the 'interaction with ccnd2' region

Full DMP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DMP1 p.Gly135Ter Pathogenic/Likely pathogenic ★★ same type
DMP1 p.Met1Val Pathogenic/Likely pathogenic ★★ same type
DMP1 c.*159T>A Uncertain significance ★★ same type
DMP1 c.*77T>C Uncertain significance ★★ same type
DMP1 p.Arg173Trp Uncertain significance ★★ ⚠ same type
DMP1 p.Arg302Ile Uncertain significance ★★ ⚠ same type
DMP1 p.Arg310Lys Uncertain significance ★★ ⚠ same type
DMP1 p.Asn233Lys Uncertain significance ★★ ⚠ same type

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-trp33ter (accessed [today's date]).

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