Is GAN p.Gln44= (c.132G>A) pathogenic?

GAN p.Gln44= (c.132G>A) is classified Conflicting classifications of pathogenicity in GAN (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2026-02-02). Very rare (popmax 0.00326%, nfe); Associated with Inborn genetic diseases.

What condition is associated with GAN p.Gln44= (c.132G>A)?

GAN p.Gln44= (c.132G>A) is associated with Inborn genetic diseases (ClinVar).

How common is GAN p.Gln44= (c.132G>A) in the general population?

GAN p.Gln44= (c.132G>A) is very rare (popmax 0.00326%, nfe) (gnomAD).

GAN p.Gln44=

c.132G>A · rs774609110 · VCV320652

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00326%, nfe)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 1.3, phastCons 1
Overall
CADD	13.84	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00326% European (non-Finnish) · 38/1,164,196 alleles

Filtering AF 0.00243% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00212%

Overall 0.00266% 42/1,578,266 alleles · very rare exomes 40/1,426,338 · genomes 2/151,928 · joint denominator

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.00657%	15,209
European (non-Finnish)grpmax	0.00326%	30,637

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Gln44=
Coding: c.132G>A
MANE Select: NM_022041
dbSNP: rs774609110
Type: single nucleotide variant
Location: chr16:81315245 (GRCh38)
Gene constraint: LOEUF 0.842 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.93 · 2 PDB
Residue 44: the btb domain

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

GAN p.Gln44Ter Uncertain significance same residue
GAN c.851+1G>A Pathogenic/Likely pathogenic ★★ same condition
GAN p.Glu486Lys Pathogenic/Likely pathogenic ★★ ⚠ same condition
GAN c.1373+4C>T Uncertain significance ★★ same condition
GAN c.283-3T>A Uncertain significance ★★ same condition
GAN p.Ala418Pro Uncertain significance ★★ ⚠ same condition
GAN p.Ala425Thr Uncertain significance ★★ ⚠ same condition
GAN p.Ala461Thr 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-gln44 (accessed [today's date]).

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