Is DYM p.Ile362del (c.1085_1087del) pathogenic?

DYM p.Ile362del (c.10851087del) is classified Uncertain significance in DYM (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-18). Very rare (popmax 8.48e-05%, nfe).

How common is DYM p.Ile362del (c.1085_1087del) in the general population?

DYM p.Ile362del (c.1085_1087del) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

DYM p.Ile362del

c.1085_1087del · rs2517953591 · VCV2099011

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

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 4.9	GERP 1.7, phastCons 1

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.48e-05% European (non-Finnish) · 1/1,179,916 alleles

Overall 6.84e-05% 1/1,461,714 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: DYM
Protein: p.Ile362del
Coding: c.1085_1087del
MANE Select: NM_001353214
dbSNP: rs2517953591
Type: Deletion
Location: chr18:49282035 (GRCh38)
Gene constraint: LOEUF 1.081 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 87.91

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

Similar variants

DYM p.Lys681fs Pathogenic/Likely pathogenic ★★ same type
DYM p.Phe41fs Pathogenic ★★ same type
DYM p.Glu123fs Pathogenic ★ same type
DYM p.Leu618_Phe619insTer Likely pathogenic ★ same type
DYM p.Pro279fs Pathogenic ★ same type
DYM p.Ser322fs Pathogenic ★ same type
DYM p.Val702fs Pathogenic ★ same type
DYM c.1626-14_1626-4del 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/dym-p-ile362del (accessed [today's date]).

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