Is APOH p.Ala160Asp (c.479C>A) pathogenic?

APOH p.Ala160Asp (c.479C>A) is classified Benign in APOH (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-02-08). AlphaMissense: likely benign (0.1081); Low-frequency (popmax 2.05%, afr).

How common is APOH p.Ala160Asp (c.479C>A) in the general population?

APOH p.Ala160Asp (c.479C>A) is low-frequency (popmax 2.05%, afr) (gnomAD).

What do computational predictors say about APOH p.Ala160Asp (c.479C>A)?

AlphaMissense predicts likely benign (score 0.1081) — an in-silico prediction, not a clinical call.

APOH p.Ala160Asp

c.479C>A · rs114459902 · VCV780447

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1081 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.05%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1081	likely benign
REVEL	0.044	moderately benign-leaning
SaProt	LLR -3.02	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.008	GERP -2.2
Regional constraint	o/e 1.01	unconstrained · MANE · 12 kb · p 0.85 · regional, not allelic
Overall
CADD	14.42	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 2.05% African / African-American · 1,535/75,018 alleles

Filtering AF 1.96% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.93%

Overall 0.105% 1,698/1,614,138 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.05%	49
Remaining individualsnot grpmax-eligible	0.136%	735
Admixed American	0.103%	968
Middle Eastern	0.0495%	2,021
European (non-Finnish)	0.0011%	90,772

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: APOH
Protein: p.Ala160Asp
Coding: c.479C>A
MANE Select: NM_000042
dbSNP: rs114459902
Type: single nucleotide variant
Location: chr17:66220679 (GRCh38)
Gene constraint: LOEUF 1.542 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.16 · 14 PDB
Residue 160: a disulfide bond; the sushi 3 domain

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

Similar variants

APOH c.64+8C>T Benign ★★ same type
APOH p.Arg154His Benign ★★ ⚠ same type
APOH p.Asn75Ser Benign ★★ same type
APOH p.Pro53= Benign ★★ same type
APOH p.Ala170Thr Uncertain significance ★ ⚠ same type
APOH p.Ala179Val Uncertain significance ★ ⚠ same type
APOH p.Ala230Thr Uncertain significance ★ ⚠ same type
APOH p.Ala333Val 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/apoh-p-ala160asp (accessed [today's date]).

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