Is APOO p.Gln49= (c.147A>G) pathogenic?

APOO p.Gln49= (c.147A>G) is classified Likely benign in APOO (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-01). Very rare (popmax 0.00296%, eas).

How common is APOO p.Gln49= (c.147A>G) in the general population?

APOO p.Gln49= (c.147A>G) is very rare (popmax 0.00296%, eas) (gnomAD).

APOO p.Gln49=

c.147A>G · rs373294515 · VCV2660172

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00296%, eas)

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 -4.3	GERP -5.2
Overall
CADD	0.065	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00296% East Asian · 1/33,812 alleles

Filtering AF 3.7e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.4e-05%

Overall 0.000331% 4/1,210,049 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00296%	33,812
Remaining individualsnot grpmax-eligible	0.0021%	47,588
European (non-Finnish)	0.000223%	447,551

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: APOO
Protein: p.Gln49=
Coding: c.147A>G
MANE Select: NM_024122
dbSNP: rs373294515
Type: single nucleotide variant
Location: chrX:23879005 (GRCh38)
Structure: AlphaFold pLDDT 74.34

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

Similar variants

APOO c.117+16T>C Benign ★★ same type
APOO p.Leu166Val Benign ★★ same type
APOO p.Ile117Thr Pathogenic ★ ⚠ same type
APOO p.Ala12Gly Uncertain significance ★ ⚠ same type
APOO p.Asp98Glu Uncertain significance ★ ⚠ same type
APOO p.Glu72Lys Uncertain significance ★ ⚠ same type
APOO p.Gly163Ala Uncertain significance ★ ⚠ same type
APOO p.Gly173Glu 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/apoo-p-gln49 (accessed [today's date]).

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