Is MAOA p.Pro496= (c.1488C>G) pathogenic?

MAOA p.Pro496= (c.1488C>G) is classified Likely benign in MAOA (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-27). Very rare (popmax 0.000335%, nfe); Associated with Brunner syndrome.

What condition is associated with MAOA p.Pro496= (c.1488C>G)?

MAOA p.Pro496= (c.1488C>G) is associated with Brunner syndrome (ClinVar).

How common is MAOA p.Pro496= (c.1488C>G) in the general population?

MAOA p.Pro496= (c.1488C>G) is very rare (popmax 0.000335%, nfe) (gnomAD).

How is Monoamine oxidase A deficiency inherited?

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

MAOA p.Pro496=

c.1488C>G · rs1569203097 · VCV792312

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000335%, nfe)

Conditions

Brunner syndrome

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 -3.4	GERP -5.7
Overall
CADD	0.31	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000335% European (non-Finnish) · 3/894,300 alleles

Filtering AF 8.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.5e-05%

Overall 0.000248% 3/1,209,995 alleles · very rare exomes 3/1,096,948 · genomes 0/113,047 · joint denominator

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: MAOA
Protein: p.Pro496=
Coding: c.1488C>G
MANE Select: NM_000240
dbSNP: rs1569203097
Type: single nucleotide variant
Location: chrX:43744417 (GRCh38)
Structure: AlphaFold pLDDT 97.09 · 4 PDB
Residue 496: an α-helix

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

Disease context

Brunner syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Monoamine oxidase A deficiency (Orphanet):

Inheritance: X-linked recessive
Onset: Childhood

Similar variants

MAOA p.Arg45Trp Pathogenic/Likely pathogenic ★★ same condition
MAOA c.796-10T>C Uncertain significance ★★ same condition
MAOA p.Ala111Thr Uncertain significance ★★ ⚠ same condition
MAOA p.Arg109Trp Uncertain significance ★★ ⚠ same condition
MAOA p.Arg45Gln Uncertain significance ★★ ⚠ same condition
MAOA p.Asn125Ser Uncertain significance ★★ ⚠ same condition
MAOA p.Asp46Gly Uncertain significance ★★ ⚠ same condition
MAOA p.Glu58Lys 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/maoa-p-pro496 (accessed [today's date]).

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