Is CYP4F2 p.Ile414= (c.1242C>T) pathogenic?

CYP4F2 p.Ile414= (c.1242C>T) is classified Likely benign in CYP4F2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-07-12). Ultra-rare (popmax 0.0759%, afr); Associated with CYP4F2-related disorder.

What condition is associated with CYP4F2 p.Ile414= (c.1242C>T)?

CYP4F2 p.Ile414= (c.1242C>T) is associated with CYP4F2-related disorder (ClinVar).

How common is CYP4F2 p.Ile414= (c.1242C>T) in the general population?

CYP4F2 p.Ile414= (c.1242C>T) is ultra-rare (popmax 0.0759%, afr) (gnomAD).

CYP4F2 p.Ile414=

c.1242C>T · rs143888844 · VCV3049482

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0759%, 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 0.6	GERP 1.8, phastCons 1
Overall
CADD	13.1	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0759% African / African-American · 57/75,052 alleles

Filtering AF 0.0601% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0544%

Overall 0.00452% 73/1,614,158 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0759%	1,317
Admixed American	0.00666%	15,006
Remaining individualsnot grpmax-eligible	0.0048%	20,833
European (non-Finnish)	0.000763%	131,112

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.Ile414=
Coding: c.1242C>T
MANE Select: NM_001082
dbSNP: rs143888844
Type: single nucleotide variant
Location: chr19:15879771 (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 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
CYP4F2 p.Arg490= 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-ile414 (accessed [today's date]).

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