Is GDAP1 p.Phe263fs (c.786del) pathogenic?

GDAP1 p.Phe263fs (c.786del) is classified Pathogenic/Likely pathogenic in GDAP1 (ClinVar, Multiple submitters, 11 submitters; last evaluated 2025-05-28). No gnomAD frequency available for this variant; Associated with Charcot-Marie-Tooth disease recessive intermediate A.

What condition is associated with GDAP1 p.Phe263fs (c.786del)?

GDAP1 p.Phe263fs (c.786del) is associated with Charcot-Marie-Tooth disease recessive intermediate A, Charcot-Marie-Tooth disease type 4A, Charcot-Marie-Tooth disease (ClinVar).

How common is GDAP1 p.Phe263fs (c.786del) in the general population?

GDAP1 p.Phe263fs (c.786del) is no gnomAD frequency available for this variant (gnomAD).

GDAP1 p.Phe263fs

Q: How is Autosomal recessive intermediate Charcot-Marie-Tooth disease type A inherited?

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

c.786del · rs1060500978 · VCV406136

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 11 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Charcot-Marie-Tooth disease recessive intermediate A

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (6 of 6) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.9	GERP 2.8, 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: GDAP1
Protein: p.Phe263fs
Coding: c.786del
MANE Select: NM_018972
dbSNP: rs1060500978
Type: Deletion
Location: chr8:74364073 (GRCh38)
Gene constraint: LOEUF 0.963 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.68 · 8 PDB
Residue 263: the gst c-terminal domain

Full GDAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Charcot-Marie-Tooth disease recessive intermediate A — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Charcot-Marie-Tooth disease type 4A Charcot-Marie-Tooth disease

For Autosomal recessive intermediate Charcot-Marie-Tooth disease type A (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood

Similar variants

GDAP1 p.Glu168fs Pathogenic/Likely pathogenic ★★ same condition
GDAP1 p.Met1fs Pathogenic/Likely pathogenic ★★ same condition
GDAP1 p.Pro179fs Pathogenic/Likely pathogenic ★★ same condition
GDAP1 p.Tyr279_Tyr280insTer Pathogenic/Likely pathogenic ★★ same condition
GDAP1 c.311-1790_408del Likely pathogenic ★ same condition
GDAP1 c.485-2del Likely pathogenic ★ same condition
GDAP1 p.Ala184fs Pathogenic ★ same condition
GDAP1 p.Ala312fs Pathogenic ★ 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/gdap1-p-phe263fs (accessed [today's date]).

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