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GeneBe

MSMO1

methylsterol monooxygenase 1, the group of Fatty acid hydroxylase domain containing

Basic information

Region (hg38): 4:165327666-165343164

Previous symbols: [ "SC4MOL" ]

Links

ENSG00000052802NCBI:6307OMIM:607545HGNC:10545Uniprot:Q15800AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • microcephaly-congenital cataract-psoriasiform dermatitis syndrome (Limited), mode of inheritance: AR
  • microcephaly-congenital cataract-psoriasiform dermatitis syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Microcephaly, congenital cataract, and psoriasiform dermatitisARAllergy/Immunology/Infectious; Biochemical; DermatologicMedical management (with oral and topical cholesterol and statin supplements,) has been described as beneficial in terms of laboratory (eg, immunocyte profiles) and clinical parameters (eg, growth, arthralgias, skin disease)Allergy/Immunology/Infectious; Biochemical; Dermatologic; Musculoskeletal; Neurologic; Ophthalmologic21285510; 24144731

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MSMO1 gene.

  • not provided (49 variants)
  • Inborn genetic diseases (7 variants)
  • Microcephaly-congenital cataract-psoriasiform dermatitis syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MSMO1 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
clinvar
1
clinvar
5
missense
1
clinvar
20
clinvar
3
clinvar
2
clinvar
26
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
4
clinvar
20
clinvar
24
Total 0 1 20 11 23

Variants in MSMO1

This is a list of pathogenic ClinVar variants found in the MSMO1 region.

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

Position Type Phenotype Significance ClinVar
4-165333022-C-G Benign (Jun 19, 2021)1240965
4-165333201-C-G Benign (Nov 12, 2018)1270307
4-165333383-G-C Likely benign (Jun 04, 2022)2047094
4-165333385-A-T not specified Uncertain significance (Feb 12, 2024)3211979
4-165333401-A-C not specified Uncertain significance (Sep 27, 2021)2405149
4-165333408-C-T not specified Uncertain significance (Sep 29, 2023)3211993
4-165333514-G-T not specified Uncertain significance (Apr 04, 2023)2532355
4-165333526-G-C Uncertain significance (Jul 05, 2022)2067401
4-165333538-A-G Uncertain significance (Jul 18, 2022)1956304
4-165333549-C-G not specified Uncertain significance (Oct 13, 2023)2191614
4-165333565-C-A Uncertain significance (Dec 21, 2023)3012308
4-165333801-A-C Benign (Nov 12, 2018)1278279
4-165333821-A-G Benign (Nov 12, 2018)1267620
4-165337753-G-A Benign (Jun 19, 2021)1252181
4-165337785-G-A Likely benign (Sep 06, 2022)1902633
4-165337815-A-G Likely benign (Oct 05, 2023)2162812
4-165337817-G-C not specified Uncertain significance (Apr 04, 2023)2517183
4-165337829-A-G Benign/Likely benign (Jan 02, 2024)742157
4-165337836-T-C Likely benign (Oct 25, 2017)728211
4-165337839-C-T Likely benign (Jun 14, 2023)1933646
4-165337848-C-A not specified Uncertain significance (Dec 21, 2023)2067304
4-165337885-T-C Uncertain significance (Feb 04, 2022)1943548
4-165337904-A-G Benign (Jan 22, 2024)783431
4-165337905-T-C Likely benign (Apr 29, 2023)1666596
4-165337909-C-G MSMO1-related condition Benign (Dec 07, 2023)728609

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MSMO1protein_codingprotein_codingENST00000261507 515538
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.09000.902125705081257130.0000318
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.5901291490.8640.000006641954
Missense in Polyphen3747.9530.77159606
Synonymous1.423648.60.7400.00000216502
Loss of Function2.32413.00.3075.48e-7180

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001520.000152
Ashkenazi Jewish0.000.00
East Asian0.0001650.000163
Finnish0.000.00
European (Non-Finnish)0.00001760.0000176
Middle Eastern0.0001650.000163
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Catalyzes the first step in the removal of the two C-4 methyl groups of 4,4-dimethylzymosterol. {ECO:0000250|UniProtKB:P53045}.;
Disease
DISEASE: Microcephaly, congenital cataract, and psoriasiform dermatitis (MCCPD) [MIM:616834]: An autosomal recessive inborn error of cholesterol metabolism characterized by accumulation of a large amount of methylsterols, particularly dimethylsterols, in affected individuals. Patients manifest psoriasiform dermatitis, arthralgias, congenital cataracts, microcephaly, and developmental delay. {ECO:0000269|PubMed:21285510, ECO:0000269|PubMed:24144731}. 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;Metabolism of lipids;zymosterol biosynthesis;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 (Consensus)

Recessive Scores

pRec
0.187

Intolerance Scores

loftool
rvis_EVS
0.7
rvis_percentile_EVS
85.42

Haploinsufficiency Scores

pHI
0.566
hipred
Y
hipred_score
0.800
ghis
0.481

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
H
gene_indispensability_pred
E
gene_indispensability_score
0.830

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Msmo1
Phenotype

Gene ontology

Biological process
fatty acid metabolic process;cholesterol biosynthetic process;steroid metabolic process;sterol biosynthetic process;oxidation-reduction process
Cellular component
endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;integral component of membrane
Molecular function
C-4 methylsterol oxidase activity;iron ion binding