Is DPM1 p.Phe51del (c.152_154del) pathogenic?

DPM1 p.Phe51del (c.152154del) is classified Uncertain significance in DPM1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-16). Very rare (popmax 0.000254%, nfe); Associated with congenital disorder of glycosylation type 1E.

What condition is associated with DPM1 p.Phe51del (c.152_154del)?

DPM1 p.Phe51del (c.152_154del) is associated with congenital disorder of glycosylation type 1E (ClinVar).

How common is DPM1 p.Phe51del (c.152_154del) in the general population?

DPM1 p.Phe51del (c.152_154del) is very rare (popmax 0.000254%, nfe) (gnomAD).

How is DPM1-CDG inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

DPM1 p.Phe51del

c.152_154del · rs2515740872 · VCV2441025

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000254%, nfe)

Conditions

congenital disorder of glycosylation type 1E

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.3	GERP 0.8, phastCons 1

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000254% European (non-Finnish) · 3/1,180,030 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000274% 4/1,461,342 alleles · very rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.00157%	63,516
European (non-Finnish)grpmax	0.000254%	393,343

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: DPM1
Protein: p.Phe51del
Coding: c.152_154del
MANE Select: NM_003859
dbSNP: rs2515740872
Type: Deletion
Location: chr20:50958370 (GRCh38)
Gene constraint: LOEUF 1.005 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 88.61

Full DPM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

congenital disorder of glycosylation type 1E — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For DPM1-CDG (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

DPM1 p.Phe51Ser Uncertain significance ★ ⚠ same residue
DPM1 p.Glu18fs Pathogenic/Likely pathogenic ★★ same condition
DPM1 p.Gly111fs Pathogenic ★★ same condition
DPM1 c.372+8del Likely benign ★★ same condition
DPM1 p.Asn57_Tyr58insTer Pathogenic ★ same condition
DPM1 p.Ile164fs Pathogenic ★ same condition
DPM1 p.Ile61fs Pathogenic ★ same condition
DPM1 c.162-3del 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/dpm1-p-phe51del (accessed [today's date]).

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