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GeneBe

SC5D

sterol-C5-desaturase, the group of Fatty acid hydroxylase domain containing

Basic information

Region (hg38): 11:121292680-121313410

Previous symbols: [ "SC5DL" ]

Links

ENSG00000109929NCBI:6309OMIM:602286HGNC:10547Uniprot:O75845AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • lathosterolosis (Definitive), mode of inheritance: AR
  • lathosterolosis (Supportive), mode of inheritance: AR
  • lathosterolosis (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
LathosterolosisARGeneralGenetic 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; Craniofacial; Gastrointestinal; Musculoskeletal; Neurologic12189593; 12812989; 17853487; 19123163
Lipid storage has been reported as being aggravated by supplemental cholesterol

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SC5D gene.

  • Lathosterolosis (131 variants)
  • not provided (63 variants)
  • Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SC5D 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
1
clinvar
13
clinvar
14
missense
32
clinvar
2
clinvar
2
clinvar
36
nonsense
2
clinvar
2
start loss
0
frameshift
2
clinvar
2
inframe indel
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
2
2
4
non coding
87
clinvar
13
clinvar
22
clinvar
122
Total 0 0 125 28 24

Variants in SC5D

This is a list of pathogenic ClinVar variants found in the SC5D region.

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

Position Type Phenotype Significance ClinVar
11-121292700-T-G Lathosterolosis Uncertain significance (Jun 14, 2016)303048
11-121292733-C-G Lathosterolosis Uncertain significance (Jun 14, 2016)303049
11-121292736-C-G Lathosterolosis Uncertain significance (Jun 14, 2016)303050
11-121301298-TA-T not specified Benign (Apr 02, 2020)873292
11-121303380-A-G Uncertain significance (Mar 14, 2022)1930429
11-121303391-C-T Benign (Jul 26, 2022)2177124
11-121303392-G-C Uncertain significance (Jul 17, 2023)1943675
11-121303397-G-A Uncertain significance (-)1050356
11-121303423-C-CTGGATGT Uncertain significance (Apr 07, 2022)2122710
11-121303432-A-G Likely benign (Sep 24, 2021)1545780
11-121303438-A-G Likely benign (May 20, 2023)2899234
11-121303441-GC-G Uncertain significance (Nov 02, 2022)2811606
11-121303461-G-A Lathosterolosis Pathogenic (Oct 01, 2002)7354
11-121303473-G-A Uncertain significance (Nov 18, 2022)2060827
11-121303481-A-T Inborn genetic diseases Uncertain significance (Apr 19, 2023)2522262
11-121303512-A-C Lathosterolosis Pathogenic (Jul 01, 2003)7356
11-121303526-A-G Lathosterolosis Uncertain significance (Jan 13, 2018)879882
11-121303537-T-C Likely benign (Mar 27, 2022)1975152
11-121303539-A-G Uncertain significance (Jun 27, 2022)1364124
11-121303544-G-C Uncertain significance (Apr 25, 2022)1394998
11-121303549-C-T Likely benign (Dec 13, 2023)731620
11-121303550-G-A Uncertain significance (Sep 24, 2021)1420238
11-121303556-G-A Lathosterolosis Uncertain significance (Apr 27, 2017)879883
11-121303564-G-T Uncertain significance (Mar 04, 2022)1369377
11-121303604-T-A Benign (Nov 19, 2023)1601729

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SC5Dprotein_codingprotein_codingENST00000264027 416242
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.002590.9391257080371257450.000147
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7211391650.8420.000008611994
Missense in Polyphen4761.1760.76827787
Synonymous0.7495158.30.8750.00000303543
Loss of Function1.66612.30.4906.73e-7140

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001740.000174
Ashkenazi Jewish0.000.00
East Asian0.0001630.000163
Finnish0.00009240.0000924
European (Non-Finnish)0.0002110.000211
Middle Eastern0.0001630.000163
South Asian0.00006530.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Catalyzes a dehydrogenation to introduce C5-6 double bond into lathosterol.;
Disease
DISEASE: Lathosterolosis (LATHST) [MIM:607330]: Autosomal recessive disorder characterized by a complex phenotype, including multiple congenital anomalies, mental retardation, and liver disease. {ECO:0000269|PubMed:12189593, ECO:0000269|PubMed:12812989}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Steroid biosynthesis - Homo sapiens (human);Simvastatin Action Pathway;Pravastatin Action Pathway;Atorvastatin Action Pathway;Hyper-IgD syndrome;Cholesteryl ester storage disease;Lysosomal Acid Lipase Deficiency (Wolman Disease);Alendronate Action Pathway;Rosuvastatin Action Pathway;Lovastatin Action Pathway;Mevalonic aciduria;Wolman disease;Risedronate Action Pathway;Cerivastatin Action Pathway;Pamidronate Action Pathway;Fluvastatin Action Pathway;Smith-Lemli-Opitz Syndrome (SLOS);Chondrodysplasia Punctata II, X Linked Dominant (CDPX2);CHILD Syndrome;Desmosterolosis;Hypercholesterolemia;Steroid Biosynthesis;Zoledronate Action Pathway;Ibandronate Action Pathway;Cholesterol Biosynthesis;Activation of gene expression by SREBF (SREBP);Metabolism of lipids;Regulation of cholesterol biosynthesis by SREBP (SREBF);Squalene and cholesterol biosynthesis;Metabolism;cholesterol biosynthesis III (via desmosterol);cholesterol biosynthesis II (via 24,25-dihydrolanosterol);superpathway of cholesterol biosynthesis;Metabolism of steroids;cholesterol biosynthesis I;Cholesterol biosynthesis via desmosterol;Steroids metabolism;Cholesterol biosynthesis via lathosterol;Cholesterol biosynthesis;Activation of gene expression by SREBF (SREBP) (Consensus)

Recessive Scores

pRec
0.151

Intolerance Scores

loftool
rvis_EVS
-0.25
rvis_percentile_EVS
35.75

Haploinsufficiency Scores

pHI
0.128
hipred
Y
hipred_score
0.551
ghis
0.481

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sc5d
Phenotype
cellular phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; respiratory system phenotype; liver/biliary system phenotype; skeleton phenotype; renal/urinary system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; digestive/alimentary phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);

Gene ontology

Biological process
lipid metabolic process;sterol biosynthetic process;cholesterol biosynthetic process via desmosterol;cholesterol biosynthetic process via lathosterol;regulation of cholesterol biosynthetic process;oxidation-reduction process
Cellular component
endoplasmic reticulum membrane;integral component of membrane
Molecular function
C-5 sterol desaturase activity;iron ion binding