SCP2

sterol carrier protein 2, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 1:52927276-53051698

Links

ENSG00000116171 ∙ NCBI:6342 ∙ OMIM:184755 ∙ HGNC:10606 ∙ Uniprot:P22307 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• sterol carrier protein 2 deficiency (Supportive), mode of inheritance: AR
• sterol carrier protein 2 deficiency (Strong), mode of inheritance: AR
• sterol carrier protein 2 deficiency (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Leukoencephalopathy with dystonia and motor neuropathy	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical; Endocrine; Genitourinary; Neurologic	16685654

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCP2 gene.

• not provided (13 variants)
• Sterol carrier protein 2 deficiency (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCP2 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			4	65	2	71
missense			143	2		145
nonsense	7					7
start loss			2			2
frameshift	6	1	2			9
inframe indel			1			1
splice donor/acceptor (+/-2bp)		7				7
splice region			9	20	1	30
non coding			4	95	40	139
Total	13	8	156	162	42

Highest pathogenic variant AF is 0.0000197

Variants in SCP2

This is a list of pathogenic ClinVar variants found in the SCP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-52927317-A-T			Benign (Aug 25, 2018)
1-52927340-C-T			Benign (Jul 17, 2018)
1-52927398-T-C			Uncertain significance (Jan 10, 2024)
1-52927401-C-T			Uncertain significance (Oct 03, 2022)
1-52927402-C-G			Likely benign (May 30, 2022)
1-52927404-C-T			Uncertain significance (May 25, 2021)
1-52927407-C-G			Uncertain significance (Jun 13, 2022)
1-52927409-C-A			Uncertain significance (Oct 04, 2022)
1-52927409-C-G			Uncertain significance (Dec 27, 2017)
1-52927410-C-T			Uncertain significance (Jul 03, 2022)
1-52927411-G-T			Conflicting classifications of pathogenicity (Nov 20, 2023)
1-52927417-G-A		SCP2-related disorder	Likely benign (Oct 06, 2023)
1-52927418-C-G		not specified	Uncertain significance (Jul 25, 2023)
1-52927431-G-T			Uncertain significance (Feb 05, 2022)
1-52927434-G-A			Uncertain significance (Oct 15, 2021)
1-52927436-G-C		not specified	Uncertain significance (Nov 08, 2022)
1-52927437-T-C			Uncertain significance (Jul 17, 2023)
1-52927451-G-C			Uncertain significance (Mar 18, 2022)
1-52927453-T-A			Uncertain significance (Oct 04, 2022)
1-52927458-T-G		not specified	Uncertain significance (Jun 16, 2023)
1-52927463-A-C		SCP2-related disorder	Uncertain significance (Feb 02, 2024)
1-52927472-C-A			Likely benign (Feb 25, 2021)
1-52927475-G-A			Likely benign (Jul 30, 2023)
1-52927477-A-T			Likely benign (Dec 06, 2023)
1-52927478-G-A			Likely benign (Aug 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCP2	protein_coding	protein_coding	ENST00000371514	16	124475

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.75e-7	0.996	125683	0	65	125748	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	226	286	0.790	0.0000135	3598
Missense in Polyphen		89	123.04	0.72334		1534
Synonymous	0.235	96	99.0	0.970	0.00000512	1017
Loss of Function	2.59	15	30.4	0.493	0.00000139	388

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000392	0.000391
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000544	0.000544
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000361	0.000352
Middle Eastern	0.000544	0.000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates in vitro the transfer of all common phospholipids, cholesterol and gangliosides between membranes. May play a role in regulating steroidogenesis. {ECO:0000269|PubMed:17157249, ECO:0000269|PubMed:8300590}.
• Disease: DISEASE: Leukoencephalopathy with dystonia and motor neuropathy (LKDMN) [MIM:613724]: A syndrome characterized by leukoencephalopathy, dystonic head tremor, spasmodic torticollis and reduced tendon reflexes in lower extremities. Additional features include hyposmia, pathologic saccadic eye movements, a slight hypoacusis, accumulation of branched-chain pristanic acid in plasma, and the presence of abnormal bile alcohol glucuronides in urine. {ECO:0000269|PubMed:16685654}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Peroxisome - Homo sapiens (human);Primary bile acid biosynthesis - Homo sapiens (human);PPAR signaling pathway - 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;PPAR Alpha Pathway;Nuclear Receptors Meta-Pathway;Mitochondrial LC-Fatty Acid Beta-Oxidation;PPAR signaling pathway;Liver steatosis AOP;DNA Damage Response (only ATM dependent);Metabolism of lipids;alpha-linolenic acid (ALA) metabolism;Metabolism of proteins;alpha-linolenic (omega3) and linoleic (omega6) acid metabolism;Beta-oxidation of pristanoyl-CoA;Peroxisomal lipid metabolism;Metabolism;Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol;Synthesis of bile acids and bile salts;Bile acid and bile salt metabolism;Peroxisomal protein import;Fatty acid metabolism;Metabolism of steroids;Bile acid biosynthesis;Phytanic acid peroxisomal oxidation;fatty acid β-oxidation (peroxisome);TYSND1 cleaves peroxisomal proteins;fatty acid β-oxidation;bile acid biosynthesis, neutral pathway (Consensus)

Recessive Scores

• pRec: 0.401

Intolerance Scores

• loftool: 0.180
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.24

Haploinsufficiency Scores

• pHI: 0.281
• hipred: Y
• hipred_score: 0.575
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.990

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scp2
• Phenotype: homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype

Gene ontology

• Biological process: protein targeting to peroxisome;steroid biosynthetic process;bile acid biosynthetic process;phospholipid transport;positive regulation of intracellular cholesterol transport;fatty acid beta-oxidation using acyl-CoA oxidase;alpha-linolenic acid metabolic process;lipid hydroperoxide transport
• Cellular component: nucleoplasm;mitochondrion;peroxisome;peroxisomal matrix;cytosol;membrane;protein-containing complex;intracellular membrane-bounded organelle
• Molecular function: fatty-acyl-CoA binding;signaling receptor binding;protein binding;cholesterol binding;propanoyl-CoA C-acyltransferase activity;long-chain fatty acyl-CoA binding;propionyl-CoA C2-trimethyltridecanoyltransferase activity;oleic acid binding