CH25H

cholesterol 25-hydroxylase, the group of Fatty acid hydroxylase domain containing

Basic information

Region (hg38): 10:89205629-89207317

Links

ENSG00000138135 ∙ NCBI:9023 ∙ OMIM:604551 ∙ HGNC:1907 ∙ Uniprot:O95992 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CH25H gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CH25H 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in CH25H

This is a list of pathogenic ClinVar variants found in the CH25H region.

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

Position	Type	Phenotype	Significance	ClinVar
10-89206478-C-T		not specified	Uncertain significance (Jan 16, 2024)
10-89206500-G-A		not specified	Uncertain significance (May 27, 2022)
10-89206583-A-C		not specified	Uncertain significance (Sep 06, 2022)
10-89206636-G-T		not specified	Uncertain significance (Jan 29, 2024)
10-89206644-C-T		not specified	Uncertain significance (Dec 21, 2022)
10-89206680-C-T		not specified	Uncertain significance (Mar 31, 2024)
10-89206682-T-C		not specified	Uncertain significance (Jun 06, 2023)
10-89206725-C-G		not specified	Uncertain significance (Apr 01, 2024)
10-89206734-T-C		not specified	Uncertain significance (Jan 13, 2023)
10-89206770-T-C		not specified	Uncertain significance (Jul 06, 2021)
10-89206814-T-C		not specified	Uncertain significance (Jun 17, 2024)
10-89206911-T-A		not specified	Uncertain significance (Oct 26, 2021)
10-89207006-A-G		not specified	Uncertain significance (Jan 18, 2022)
10-89207028-C-T		not specified	Uncertain significance (Jun 10, 2024)
10-89207036-G-A		not specified	Uncertain significance (Sep 17, 2021)
10-89207078-T-C		not specified	Uncertain significance (Mar 23, 2022)
10-89207081-T-C		not specified	Uncertain significance (Jan 24, 2023)
10-89207105-G-C		not specified	Uncertain significance (Nov 07, 2022)
10-89207148-C-T		not specified	Uncertain significance (Sep 27, 2021)
10-89207255-C-A		not specified	Uncertain significance (Oct 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CH25H	protein_coding	protein_coding	ENST00000371852	1	1378

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.227	0.741	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.382	135	148	0.912	0.00000711	1773
Missense in Polyphen		39	57.44	0.67896		708
Synonymous	0.0337	70	70.4	0.995	0.00000363	564
Loss of Function	1.80	2	7.21	0.277	3.16e-7	62

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the formation of 25-hydroxycholesterol from cholesterol, leading to repress cholesterol biosynthetic enzymes (PubMed:9852097). Plays a key role in cell positioning and movement in lymphoid tissues: 25-hydroxycholesterol is an intermediate in biosynthesis of 7-alpha,25-dihydroxycholesterol (7-alpha,25-OHC), an oxysterol that acts as a ligand for the G protein-coupled receptor GPR183/EBI2, a chemotactic receptor for a number of lymphoid cells. May play an important role in regulating lipid metabolism by synthesizing a corepressor that blocks sterol regulatory element binding protein (SREBP) processing. In testis, production of 25-hydroxycholesterol by macrophages may play a role in Leydig cell differentiation. {ECO:0000250|UniProtKB:Q9Z0F5, ECO:0000269|PubMed:9852097}.
• Pathway: Primary bile acid biosynthesis - Homo sapiens (human);27-Hydroxylase Deficiency;Bile Acid Biosynthesis;Congenital Bile Acid Synthesis Defect Type II;Cerebrotendinous Xanthomatosis (CTX);Zellweger Syndrome;Familial Hypercholanemia (FHCA);Congenital Bile Acid Synthesis Defect Type III;Metabolism of lipids;Metabolism;Synthesis of bile acids and bile salts;Bile acid and bile salt metabolism;Metabolism of steroids (Consensus)

Recessive Scores

• pRec: 0.172

Intolerance Scores

• loftool: 0.344
• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

• pHI: 0.0742
• hipred: N
• hipred_score: 0.404
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.195

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ch25h
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: lipid metabolic process;bile acid biosynthetic process;cholesterol metabolic process;sterol biosynthetic process;B cell chemotaxis;oxidation-reduction process
• Cellular component: endoplasmic reticulum membrane;cytosol;integral component of membrane
• Molecular function: C-4 methylsterol oxidase activity;cholesterol 25-hydroxylase activity;iron ion binding;steroid hydroxylase activity