Is MAOB p.Ser488= (c.1464C>T) pathogenic?

MAOB p.Ser488= (c.1464C>T) is classified Likely benign in MAOB (ClinVar, Single submitter, 1 submitter; last evaluated 2018-03-06). Very rare (popmax 0.00525%, afr).

How common is MAOB p.Ser488= (c.1464C>T) in the general population?

MAOB p.Ser488= (c.1464C>T) is very rare (popmax 0.00525%, afr) (gnomAD).

MAOB p.Ser488=

c.1464C>T · rs763123042 · VCV728050

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00525%, afr)

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 -5.2	GERP -3.8
Overall
CADD	0.033	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00525% African / African-American · 3/57,136 alleles

Filtering AF 0.00171% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00143%

Overall 0.00248% 30/1,208,594 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00525%	19,045
Remaining individualsnot grpmax-eligible	0.00421%	23,770
East Asian	0.00297%	33,699
European (non-Finnish)	0.00257%	38,890
South Asian	0.00177%	56,590

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: MAOB
Protein: p.Ser488=
Coding: c.1464C>T
MANE Select: NM_000898
dbSNP: rs763123042
Type: single nucleotide variant
Location: chrX:43767565 (GRCh38)
Structure: AlphaFold pLDDT 95.68 · 57 PDB
Residue 488: an α-helix

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

Similar variants

MAOB p.Ala161Ser Uncertain significance ★★ ⚠ same type
MAOB p.Ala322Thr Uncertain significance ★ ⚠ same type
MAOB p.Arg100Ser Uncertain significance ★ ⚠ same type
MAOB p.Arg220Gln Uncertain significance ★ ⚠ same type
MAOB p.Arg242Lys Uncertain significance ★ ⚠ same type
MAOB p.Arg282Lys Uncertain significance ★ ⚠ same type
MAOB p.Arg288His Uncertain significance ★ ⚠ same type
MAOB p.Arg36Trp 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/maob-p-ser488 (accessed [today's date]).

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