FAXDC2

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

Basic information

Region (hg38): 5:154818492-154859252

Previous symbols: [ "C5orf4" ]

Links

ENSG00000170271 ∙ NCBI:10826 ∙ OMIM:619853 ∙ HGNC:1334 ∙ Uniprot:Q96IV6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FAXDC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAXDC2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	0

Variants in FAXDC2

This is a list of pathogenic ClinVar variants found in the FAXDC2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-154820342-G-A		not specified	Uncertain significance (Dec 11, 2024)
5-154820368-C-T		not specified	Uncertain significance (May 26, 2024)
5-154820388-C-G		not specified	Uncertain significance (Dec 15, 2023)
5-154820402-TC-T		Autism	Uncertain significance (-)
5-154820429-G-C		not specified	Uncertain significance (Jan 10, 2022)
5-154820444-C-T		not specified	Uncertain significance (Aug 01, 2024)
5-154820455-C-T		not specified	Uncertain significance (Nov 28, 2023)
5-154821273-A-T		not specified	Uncertain significance (May 15, 2024)
5-154821276-C-T		not specified	Uncertain significance (Oct 23, 2024)
5-154821290-G-A		not specified	Uncertain significance (Dec 01, 2022)
5-154821356-C-A		not specified	Uncertain significance (Nov 05, 2021)
5-154821386-A-G		not specified	Uncertain significance (Jul 20, 2022)
5-154821411-G-T		not specified	Uncertain significance (Jan 30, 2025)
5-154822483-T-C		not specified	Likely benign (May 20, 2024)
5-154822489-G-A		not specified	Uncertain significance (Oct 25, 2024)
5-154822557-A-G		not specified	Uncertain significance (Jul 12, 2022)
5-154823415-C-T		not specified	Uncertain significance (Jun 24, 2022)
5-154823417-A-T		not specified	Uncertain significance (Oct 21, 2021)
5-154823423-G-A		not specified	Uncertain significance (Feb 07, 2023)
5-154823474-C-T		not specified	Uncertain significance (Dec 13, 2024)
5-154823484-C-G		not specified	Uncertain significance (Sep 27, 2024)
5-154823511-G-A		not specified	Uncertain significance (Aug 12, 2024)
5-154823538-T-C		not specified	Likely benign (Mar 15, 2024)
5-154823592-C-T		not specified	Uncertain significance (Mar 01, 2025)
5-154830815-C-T		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAXDC2	protein_coding	protein_coding	ENST00000326080	8	40762

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.72e-8	0.409	124722	0	98	124820	0.000393

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.596	162	185	0.877	0.00000956	2183
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000440	0.000426
Ashkenazi Jewish	0.0000994	0.0000993
East Asian	0.000223	0.000222
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000393	0.000388
Middle Eastern	0.000223	0.000222
South Asian	0.00115	0.00114
Other	0.000333	0.000329

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0955

Intolerance Scores

• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.9

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.296
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Gene ontology

• Biological process: sterol biosynthetic process;oxidation-reduction process
• Cellular component: endoplasmic reticulum membrane;integral component of membrane
• Molecular function: C-4 methylsterol oxidase activity;iron ion binding