Is APOO p.Ser162= (c.486T>C) pathogenic?

APOO p.Ser162= (c.486T>C) is classified Likely benign in APOO (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-07-14). Very rare (popmax 0.00135%, nfe); Associated with APOO-related disorder.

What condition is associated with APOO p.Ser162= (c.486T>C)?

APOO p.Ser162= (c.486T>C) is associated with APOO-related disorder (ClinVar).

How common is APOO p.Ser162= (c.486T>C) in the general population?

APOO p.Ser162= (c.486T>C) is very rare (popmax 0.00135%, nfe) (gnomAD).

APOO p.Ser162=

c.486T>C · rs750609010 · VCV3036211

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00135%, nfe)

Conditions

APOO-related disorder

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 0.45	GERP -4.4, phastCons 0.38
Overall
CADD	8.449	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00135% European (non-Finnish) · 12/887,345 alleles

Filtering AF 0.000721% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000569%

Overall 0.001% 12/1,199,351 alleles · very rare

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.Ser162=
Coding: c.486T>C
MANE Select: NM_024122
dbSNP: rs750609010
Type: single nucleotide variant
Location: chrX:23856377 (GRCh38)
Structure: AlphaFold pLDDT 74.34

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

Disease context

APOO-related disorder

Similar variants

APOO p.Ile117Thr Pathogenic ★ ⚠ same condition
APOO p.Ser15Cys Likely benign same condition
APOO c.117+16T>C Benign ★★ same type
APOO p.Leu166Val Benign ★★ 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

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-ser162 (accessed [today's date]).

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