FAXDC2

protein-coding

fatty acid hydroxylase domain containing 2, the group of Fatty acid hydroxylase domain containing

Gene summary

Predicted to enable C-4 methylsterol oxidase activity. Involved in positive regulation of megakaryocyte differentiation and positive regulation of protein phosphorylation. Located in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C5orf4

MANE transcript

NM_032385.5

Inheritance

—

ClinVar variants

U:46B:2

Top phenotype

Autism

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr5:154,818,492-154,859,252

External References & Databases

Ensembl (ENSG00000170271)

Transcript & Mutation Effects

hg38 • Region Span ~40.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

schizophreniaNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0005090

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FAXDC2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 40

not providedTotal: 1

AutismTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032385.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			42 clinvar	2 clinvar		44
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	46	2	0	48

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032385.5	RefSeq	NP_115761.2	8	MANE Select
ENST00000326080.10	Ensembl	ENSP00000320604.5	8	MANE Select
ENST00000517938.5	Ensembl	ENSP00000430286.1	7	Standard
ENST00000517938.6	Ensembl	ENSP00000430286.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

sterol biosynthetic process
oxidation-reduction process

Molecular Function

C-4 methylsterol oxidase activity
iron ion binding

Cellular Component

endoplasmic reticulum membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000326080
Coding exons: 8
Length: 40762
Individuals with no LoFs: 124722
Homozygous LoFs: 0
Heterozygous LoFs: 98
Defined: 124820
p: 0.000393

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.596	162	185	0.877	0.00000956	2183
Missense (PolyPhen)		56	59.748	0.93727		712
Synonymous	-1.24	82	68.9	1.19	0.00000362	625
Loss of Function	0.846	14	17.9	0.784	8.47e-7	195

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00021	0.00019	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00039	0.00039	rare
South Asian	0.0012	0.0011	notable
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0955

Intolerance Scores

RVIS EVS: 0.64
RVIS percentile EVS: 83.9

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium