Is MAOA p.Pro413Ser (c.1237C>T) pathogenic?

MAOA p.Pro413Ser (c.1237C>T) is classified Uncertain significance in MAOA (ClinVar, Single submitter, 1 submitter; last evaluated 2020-02-14). AlphaMissense: ambiguous (0.4776); Absent from gnomAD v4.1.

How common is MAOA p.Pro413Ser (c.1237C>T) in the general population?

MAOA p.Pro413Ser (c.1237C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MAOA p.Pro413Ser (c.1237C>T)?

AlphaMissense predicts ambiguous (score 0.4776) — an in-silico prediction, not a clinical call.

MAOA p.Pro413Ser

c.1237C>T · rs2033963994 · VCV916065

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4776 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
AlphaMissense	0.4776	ambiguous
REVEL	0.514	indeterminate
SaProt	LLR -11.48	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2.9, phastCons 1
Regional constraint	o/e 0.45	unconstrained · MANE · 13 kb · p 4e-14 · regional, not allelic
Overall
CADD	24.9	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: MAOA
Protein: p.Pro413Ser
Coding: c.1237C>T
MANE Select: NM_000240
dbSNP: rs2033963994
Type: single nucleotide variant
Location: chrX:43742022 (GRCh38)
Structure: AlphaFold pLDDT 97.09 · 4 PDB

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

Similar variants

MAOA p.Arg45Trp Pathogenic/Likely pathogenic ★★ same type
MAOA c.1262+3A>G Uncertain significance ★★ same type
MAOA c.796-10T>C Uncertain significance ★★ same type
MAOA p.Ala111Thr Uncertain significance ★★ ⚠ same type
MAOA p.Arg109Trp Uncertain significance ★★ ⚠ same type
MAOA p.Arg45Gln Uncertain significance ★★ ⚠ same type
MAOA p.Asn125Ser Uncertain significance ★★ ⚠ same type
MAOA p.Asp46Gly Uncertain significance ★★ ⚠ same type

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-pro413ser (accessed [today's date]).

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