Menu
GeneBe

SCP2

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

Basic information

Region (hg38): 1:52927275-53051698

Links

ENSG00000116171NCBI:6342OMIM:184755HGNC:10606Uniprot:P22307AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Leukoencephalopathy with dystonia and motor neuropathyARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingBiochemical; Endocrine; Genitourinary; Neurologic16685654

ClinVar

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

  • not provided (378 variants)
  • Inborn genetic diseases (12 variants)
  • Sterol carrier protein 2 deficiency (10 variants)
  • not specified (3 variants)
  • SCP2-related condition (2 variants)
  • Leukodystrophy (1 variants)
  • Sensorineural hearing loss disorder (1 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
5
clinvar
52
clinvar
2
clinvar
59
missense
139
clinvar
2
clinvar
141
nonsense
7
clinvar
7
start loss
2
clinvar
2
frameshift
6
clinvar
1
clinvar
2
clinvar
9
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
4
clinvar
4
splice region
10
17
1
28
non coding
4
clinvar
80
clinvar
40
clinvar
124
Total 13 5 153 134 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)1296645
1-52927340-C-T Benign (Jul 17, 2018)1227815
1-52927398-T-C Uncertain significance (Jan 10, 2024)2068347
1-52927401-C-T Uncertain significance (Oct 03, 2022)1483727
1-52927402-C-G Likely benign (May 30, 2022)2001063
1-52927404-C-T Uncertain significance (May 25, 2021)1471293
1-52927407-C-G Uncertain significance (Jun 13, 2022)1477615
1-52927409-C-A Uncertain significance (Oct 04, 2022)2097480
1-52927409-C-G Uncertain significance (Dec 27, 2017)595570
1-52927410-C-T Uncertain significance (Jul 03, 2022)2000819
1-52927411-G-T Conflicting classifications of pathogenicity (Nov 20, 2023)596443
1-52927417-G-A Likely benign (Oct 06, 2023)1659928
1-52927418-C-G Inborn genetic diseases Uncertain significance (Jul 25, 2023)2602482
1-52927431-G-T Uncertain significance (Feb 05, 2022)1479392
1-52927434-G-A Uncertain significance (Oct 15, 2021)1496077
1-52927436-G-C Inborn genetic diseases Uncertain significance (Nov 08, 2022)2060975
1-52927437-T-C Uncertain significance (Jul 17, 2023)1901842
1-52927451-G-C Uncertain significance (Mar 18, 2022)839307
1-52927453-T-A Uncertain significance (Oct 04, 2022)1475368
1-52927458-T-G Inborn genetic diseases Uncertain significance (Jun 16, 2023)1996240
1-52927463-A-C SCP2-related condition Uncertain significance (Feb 02, 2024)3036323
1-52927472-C-A Likely benign (Feb 25, 2021)1537295
1-52927475-G-A Likely benign (Jul 30, 2023)1632502
1-52927477-A-T Likely benign (Dec 06, 2023)2819441
1-52927478-G-A Likely benign (Aug 09, 2022)2052889

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SCP2protein_codingprotein_codingENST00000371514 16124475
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
8.75e-70.9961256830651257480.000258
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.262262860.7900.00001353598
Missense in Polyphen89123.040.723341534
Synonymous0.2359699.00.9700.000005121017
Loss of Function2.591530.40.4930.00000139388

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003920.000391
Ashkenazi Jewish0.00009930.0000992
East Asian0.0005440.000544
Finnish0.0001850.000185
European (Non-Finnish)0.0003610.000352
Middle Eastern0.0005440.000544
South Asian0.00006530.0000653
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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