Is CYP4F2 p.Arg490= (c.1470C>T) pathogenic?

CYP4F2 p.Arg490= (c.1470C>T) is classified Likely benign in CYP4F2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-09-13). Rare (popmax 0.212%, afr); Associated with CYP4F2-related disorder.

What condition is associated with CYP4F2 p.Arg490= (c.1470C>T)?

CYP4F2 p.Arg490= (c.1470C>T) is associated with CYP4F2-related disorder (ClinVar).

How common is CYP4F2 p.Arg490= (c.1470C>T) in the general population?

CYP4F2 p.Arg490= (c.1470C>T) is rare (popmax 0.212%, afr) (gnomAD).

CYP4F2 p.Arg490=

c.1470C>T · rs150488576 · VCV3054703

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.212%, afr)

Conditions

CYP4F2-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 -20	GERP -2.9
Overall
CADD	5.932	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.212% African / African-American · 159/75,034 alleles

Filtering AF 0.185% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.175%

Overall 0.0118% 191/1,614,034 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.212%	472
Remaining individualsnot grpmax-eligible	0.0192%	5,208
Admixed American	0.0167%	6,001
Middle Eastern	0.0165%	6,052
South Asian	0.0011%	91,066
European (non-Finnish)	0.000678%	147,499

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: CYP4F2
Protein: p.Arg490=
Coding: c.1470C>T
MANE Select: NM_001082
dbSNP: rs150488576
Type: single nucleotide variant
Location: chr19:15878864 (GRCh38)
Gene constraint: LOEUF 1.197 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.97

Full CYP4F2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CYP4F2-related disorder

Similar variants

CYP4F2 p.Arg490His Uncertain significance ★ ⚠ same residue
CYP4F2 c.1398-4C>G Benign same condition
CYP4F2 c.343+6A>G Likely benign same condition
CYP4F2 c.919-9T>G Likely benign same condition
CYP4F2 c.*8A>G Likely benign same condition
CYP4F2 p.Ala16Pro Benign ⚠ same condition
CYP4F2 p.Ala82= Benign same condition
CYP4F2 p.Arg275= Likely benign 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/cyp4f2-p-arg490 (accessed [today's date]).

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