Is MAOA p.Val244= (c.732C>T) pathogenic?

MAOA p.Val244= (c.732C>T) is classified Likely benign in MAOA (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-03-08). Very rare (popmax 0.00176%, sas); Associated with Brunner syndrome.

What condition is associated with MAOA p.Val244= (c.732C>T)?

MAOA p.Val244= (c.732C>T) is associated with Brunner syndrome (ClinVar).

How common is MAOA p.Val244= (c.732C>T) in the general population?

MAOA p.Val244= (c.732C>T) is very rare (popmax 0.00176%, sas) (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.Val244=

c.732C>T · rs980804164 · VCV720971

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00176%, sas)

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 -1.1	GERP 0.86, phastCons 0.001
Overall
CADD	3.915	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00176% South Asian · 1/56,928 alleles

Filtering AF 0.000164% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000119%

Overall 0.000639% 7/1,094,844 alleles · very rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0021%	47,547
South Asiangrpmax	0.00176%	56,928
European (non-Finnish)	0.00056%	178,522

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: MAOA
Protein: p.Val244=
Coding: c.732C>T
MANE Select: NM_000240
dbSNP: rs980804164
Type: single nucleotide variant
Location: chrX:43731327 (GRCh38)
Structure: AlphaFold pLDDT 97.09 · 4 PDB
Residue 244: a β-strand

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.Val244Ile Likely pathogenic ★ ⚠ same residue
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

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-val244 (accessed [today's date]).

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