Is GAN p.Asp9= (c.27C>T) pathogenic?

GAN p.Asp9= (c.27C>T) is classified Likely benign in GAN (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-13). Very rare (popmax 0.00143%, afr); Associated with giant axonal neuropathy 1.

What condition is associated with GAN p.Asp9= (c.27C>T)?

GAN p.Asp9= (c.27C>T) is associated with giant axonal neuropathy 1 (ClinVar).

How common is GAN p.Asp9= (c.27C>T) in the general population?

GAN p.Asp9= (c.27C>T) is very rare (popmax 0.00143%, afr) (gnomAD).

How is Giant axonal neuropathy inherited?

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

GAN p.Asp9=

c.27C>T · rs777103014 · VCV1654113

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00143%, 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	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.19	GERP 0.45, phastCons 0.36
Overall
CADD	11.98	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00143% African / African-American · 1/70,138 alleles

Filtering AF 0.000255% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000164%

Overall 0.000521% 8/1,534,560 alleles · very rare exomes 6/1,382,374 · genomes 2/152,186 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00143%	70,138
European (non-Finnish)	0.000613%	163,158

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.Asp9=
Coding: c.27C>T
MANE Select: NM_022041
dbSNP: rs777103014
Type: single nucleotide variant
Location: chr16:81315140 (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 p.Asp9Glu Uncertain significance ★ ⚠ same residue
GAN p.Asp9Tyr Uncertain significance ★ ⚠ same residue
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

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-asp9 (accessed [today's date]).

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