Is GAN p.Ile413= (c.1239C>T) pathogenic?

GAN p.Ile413= (c.1239C>T) is classified Benign/Likely benign in GAN (ClinVar, Multiple submitters, 8 submitters; last evaluated 2026-01-27). Low-frequency (popmax 1.91%, afr); Associated with giant axonal neuropathy 1.

What condition is associated with GAN p.Ile413= (c.1239C>T)?

GAN p.Ile413= (c.1239C>T) is associated with giant axonal neuropathy 1 (ClinVar).

How common is GAN p.Ile413= (c.1239C>T) in the general population?

GAN p.Ile413= (c.1239C>T) is low-frequency (popmax 1.91%, afr) (gnomAD).

How is Giant axonal neuropathy inherited?

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

GAN p.Ile413=

c.1239C>T · rs61740238 · VCV261479

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.91%, afr)

Conditions

giant axonal neuropathy 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.87 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.78	GERP -4.2, phastCons 0.018
Overall
CADD	5.055	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.91% African / African-American · 1,431/75,000 alleles

Filtering AF 1.83% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.79%

Overall 0.0999% 1,613/1,613,822 alleles · low-frequency exomes 768/1,461,598 · genomes 845/152,224 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.91%	52
Remaining individualsnot grpmax-eligible	0.134%	744
Admixed American	0.0866%	1,154
Middle Eastern	0.0495%	2,021
European (non-Finnish)	0.00348%	28,775
Finnishnot grpmax-eligible	0.00156%	63,988
South Asian	0.0011%	91,074

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: GAN
Protein: p.Ile413=
Coding: c.1239C>T
MANE Select: NM_022041
dbSNP: rs61740238
Type: single nucleotide variant
Location: chr16:81364976 (GRCh38)
Gene constraint: LOEUF 0.842 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.93 · 2 PDB

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

Disease context

giant axonal neuropathy 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Giant axonal neuropathy (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy

Similar variants

GAN c.1502+1G>T Pathogenic/Likely pathogenic ★★ same condition
GAN c.851+1G>A Pathogenic/Likely pathogenic ★★ same condition
GAN p.Arg545His Pathogenic/Likely pathogenic ★★ same condition
GAN p.Gln103Ter Pathogenic ★★ same condition
GAN p.Glu486Lys Pathogenic/Likely pathogenic ★★ ⚠ same condition
GAN c.1373+4C>T Uncertain significance ★★ same condition
GAN c.1612+4A>G Uncertain significance ★★ same condition
GAN c.283-3T>A 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/gan-p-ile413 (accessed [today's date]).

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