MVD

mevalonate diphosphate decarboxylase

Basic information

Region (hg38): 16:88651935-88663161

Links

ENSG00000167508 ∙ NCBI:4597 ∙ OMIM:603236 ∙ HGNC:7529 ∙ Uniprot:P53602 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• porokeratosis 7, multiple types (Strong), mode of inheritance: AD
• disseminated superficial actinic porokeratosis (Supportive), mode of inheritance: AD
• porokeratosis 7, multiple types (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Porokeratosis 7, multiple types	AD	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	Dermatologic	22983302

ClinVar

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

• Porokeratosis 7, multiple types (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MVD 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				3	2	5
missense	1		39	3	1	44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)	2					2
splice region			1		1	2
non coding				2	1	3
Total	3	0	39	8	4

Highest pathogenic variant AF is 0.0000263

Variants in MVD

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

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

Position	Type	Phenotype	Significance	ClinVar
16-88651945-C-T		Granulomatous disease, chronic, autosomal recessive, cytochrome b-negative	Benign (Jan 12, 2024)
16-88652532-G-C		not specified	Uncertain significance (Apr 04, 2024)
16-88652541-G-C		not specified	Uncertain significance (Aug 12, 2024)
16-88652541-G-T		not specified	Uncertain significance (Oct 07, 2024)
16-88652569-C-T		not specified	Uncertain significance (Sep 11, 2024)
16-88652592-G-T		Nonsyndromic hearing impairment	Uncertain significance (-)
16-88653302-G-T		not specified	Uncertain significance (Nov 25, 2024)
16-88653318-T-C			Benign/Likely benign (Nov 01, 2023)
16-88653337-G-A			Uncertain significance (-)
16-88653352-G-A			Likely benign (Jun 01, 2023)
16-88653362-G-C		not specified	Uncertain significance (Jan 18, 2023)
16-88653367-G-C			Uncertain significance (-)
16-88653416-A-C		MVD-related disorder	Benign (Jan 06, 2020)
16-88654687-C-A		Porokeratosis 7, multiple types	Uncertain significance (Mar 12, 2021)
16-88654691-C-A		Porokeratosis 7, multiple types	Pathogenic (Aug 01, 2019)
16-88654693-T-C		not specified	Likely benign (Jul 05, 2023)
16-88654703-C-T		MVD-related disorder	Likely benign (Jun 19, 2019)
16-88654704-G-A		not specified	Uncertain significance (May 02, 2023)
16-88654731-G-A		not specified	Uncertain significance (Jun 04, 2024)
16-88654746-G-A		not specified	Uncertain significance (May 18, 2023)
16-88654803-G-A		not specified	Uncertain significance (May 26, 2024)
16-88655210-C-T		not specified	Uncertain significance (Mar 18, 2024)
16-88655221-T-C		Porokeratosis 7, multiple types	Pathogenic (-)
16-88655222-T-G		not specified	Uncertain significance (Jun 02, 2023)
16-88655280-CGGGAA-C		Linear porokeratosis	Likely pathogenic (May 01, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MVD	protein_coding	protein_coding	ENST00000301012	10	11227

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.74e-17	0.00122	125657	0	51	125708	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.363	286	269	1.06	0.0000188	2502
Missense in Polyphen		80	81.565	0.98081		778
Synonymous	-1.20	136	119	1.14	0.00000862	838
Loss of Function	-0.862	23	18.9	1.21	9.87e-7	202

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000309	0.000302
Ashkenazi Jewish	0.000207	0.000199
East Asian	0.000360	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000101	0.0000967
Middle Eastern	0.000360	0.000326
South Asian	0.000872	0.000817
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Performs the first committed step in the biosynthesis of isoprenes.
• Pathway: Mevalonate pathway;Terpenoid backbone 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;Sterol Regulatory Element-Binding Proteins (SREBP) signalling;Activation of gene expression by SREBF (SREBP);Metabolism of lipids;Post-translational protein modification;Metabolism of proteins;Regulation of cholesterol biosynthesis by SREBP (SREBF);Metabolism;superpathway of cholesterol biosynthesis;Metabolism of steroids;Synthesis of Dolichyl-phosphate;Synthesis of substrates in N-glycan biosythesis;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation;Steroids metabolism;Cholesterol biosynthesis;Activation of gene expression by SREBF (SREBP);mevalonate pathway;superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) (Consensus)

Recessive Scores

• pRec: 0.198

Intolerance Scores

• rvis_EVS: -1.06
• rvis_percentile_EVS: 7.52

Haploinsufficiency Scores

• pHI: 0.308
• hipred: N
• hipred_score: 0.197
• ghis: 0.483

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.999

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mvd

Gene ontology

• Biological process: dolichyl diphosphate biosynthetic process;cholesterol biosynthetic process;positive regulation of cell population proliferation;isoprenoid biosynthetic process;isopentenyl diphosphate biosynthetic process, mevalonate pathway;regulation of cholesterol biosynthetic process
• Cellular component: peroxisome;cytosol
• Molecular function: diphosphomevalonate decarboxylase activity;ATP binding;Hsp70 protein binding;protein homodimerization activity