Is DYM p.Phe41fs (c.122del) pathogenic?

DYM p.Phe41fs (c.122del) is classified Pathogenic in DYM (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-03-29). Absent from gnomAD.

How common is DYM p.Phe41fs (c.122del) in the general population?

DYM p.Phe41fs (c.122del) is absent from gnomAD (gnomAD).

DYM p.Phe41fs

c.122del · rs794727290 · VCV195317

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 18
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.4	GERP 0.96, phastCons 1

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DYM
Protein: p.Phe41fs
Coding: c.122del
MANE Select: NM_001353214
dbSNP: rs794727290
Type: Deletion
Location: chr18:49430273 (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.Phe41= Likely benign ★ same residue
DYM p.Lys681fs Pathogenic/Likely 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-phe41fs (accessed [today's date]).

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