Is APOA5 p.Thr55= (c.165C>G) pathogenic?

APOA5 p.Thr55= (c.165C>G) is classified Benign/Likely benign in APOA5 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-02-03). Rare (popmax 0.173%, nfe); Associated with Cardiovascular phenotype.

What condition is associated with APOA5 p.Thr55= (c.165C>G)?

APOA5 p.Thr55= (c.165C>G) is associated with Cardiovascular phenotype (ClinVar).

How common is APOA5 p.Thr55= (c.165C>G) in the general population?

APOA5 p.Thr55= (c.165C>G) is rare (popmax 0.173%, nfe) (gnomAD).

APOA5 p.Thr55=

c.165C>G · rs138300114 · VCV779436

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.173%, nfe)

Conditions

Cardiovascular phenotype

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 0.16	GERP 1, phastCons 0.051
Overall
CADD	6.455	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.173% European (non-Finnish) · 2,036/1,179,390 alleles

Filtering AF 0.166% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.164%

Overall 0.135% 2,170/1,609,590 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.173%	579
Remaining individualsnot grpmax-eligible	0.119%	843
Admixed American	0.0351%	2,849
African / African-American	0.0307%	3,256
Finnishnot grpmax-eligible	0.0231%	4,336
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,572
East Asian	0.00223%	44,848

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: APOA5
Protein: p.Thr55=
Coding: c.165C>G
MANE Select: NM_001371904
dbSNP: rs138300114
Type: single nucleotide variant
Location: chr11:116791064 (GRCh38)
Gene constraint: LOEUF 1.146 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.38
Residue 55: a modified residue (phosphothreonine; by fam20c)

Full APOA5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

APOA5 c.161+3G>A Uncertain significance ★★ same condition
APOA5 c.161+5G>C Uncertain significance ★★ same condition
APOA5 p.Ala244Ser Uncertain significance ★★ ⚠ same condition
APOA5 p.Ala302Val Uncertain significance ★★ ⚠ same condition
APOA5 p.Ala82Val Uncertain significance ★★ ⚠ same condition
APOA5 p.Arg226Cys Uncertain significance ★★ ⚠ same condition
APOA5 p.Arg233Gln Uncertain significance ★★ ⚠ same condition
APOA5 p.Arg40Gly Uncertain significance ★★ ⚠ same condition

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/apoa5-p-thr55 (accessed [today's date]).

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