Is APOOL p.Phe244Leu (c.732T>A) pathogenic?

APOOL p.Phe244Leu (c.732T>A) is classified Uncertain significance in APOOL (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-05). AlphaMissense: likely pathogenic (0.8103); Very rare (popmax 0.00224%, amr).

How common is APOOL p.Phe244Leu (c.732T>A) in the general population?

APOOL p.Phe244Leu (c.732T>A) is very rare (popmax 0.00224%, amr) (gnomAD).

What do computational predictors say about APOOL p.Phe244Leu (c.732T>A)?

AlphaMissense predicts likely pathogenic (score 0.8103) — an in-silico prediction, not a clinical call.

APOOL p.Phe244Leu

c.732T>A · rs1457694192 · VCV2524195

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8103 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00224%, amr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8103	likely pathogenic · top 4% in APOOL
REVEL	0.194	benign-leaning
SaProt	LLR -5.42	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.3	GERP 0.99, phastCons 1
Regional constraint	o/e 1.06	unconstrained · MANE · 84 kb · p 0.38 · regional, not allelic
Overall
CADD	22.3	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

Grpmax group 0.00224% Admixed American · 1/44,723 alleles

Overall 8.33e-05% 1/1,201,049 alleles · very rare exomes 1/1,087,750 · genomes 0/113,299 · joint denominator

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: APOOL
Protein: p.Phe244Leu
Coding: c.732T>A
MANE Select: NM_198450
dbSNP: rs1457694192
Type: single nucleotide variant
Location: chrX:85087603 (GRCh38)
Structure: AlphaFold pLDDT 70.83
Residue 244: the 'disordered' region

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

Similar variants

APOOL p.Ala124Glu Uncertain significance ★ ⚠ same type
APOOL p.Ala178Gly Uncertain significance ★ ⚠ same type
APOOL p.Ala241Ser Uncertain significance ★ ⚠ same type
APOOL p.Arg69Cys Uncertain significance ★ ⚠ same type
APOOL p.Arg69His Uncertain significance ★ ⚠ same type
APOOL p.Gln156His Uncertain significance ★ same type
APOOL p.Gln173His Uncertain significance ★ ⚠ same type
APOOL p.Glu30Lys 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/apool-p-phe244leu (accessed [today's date]).

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