MDP1

magnesium dependent phosphatase 1, the group of HAD Asp-based protein phosphatases

Basic information

Region (hg38): 14:24213942-24216070

Links

ENSG00000213920 ∙ NCBI:145553 ∙ ∙ HGNC:28781 ∙ Uniprot:Q86V88 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MDP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MDP1 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						0
missense			10	2		12
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	0

Variants in MDP1

This is a list of pathogenic ClinVar variants found in the MDP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-24214070-G-C		not specified	Uncertain significance (Mar 19, 2024)
14-24214076-G-A		not specified	Uncertain significance (Nov 09, 2021)
14-24214099-T-C		not specified	Likely benign (Dec 11, 2023)
14-24214105-T-G		not specified	Likely benign (May 14, 2024)
14-24214109-G-A		not specified	Uncertain significance (Apr 27, 2022)
14-24214124-C-T		not specified	Uncertain significance (Feb 09, 2023)
14-24214135-G-A		not specified	Likely benign (Dec 28, 2023)
14-24214313-G-C		Malignant tumor of prostate	Uncertain significance (-)
14-24214314-T-A		not specified	Uncertain significance (Jul 19, 2022)
14-24214336-C-T		not specified	Uncertain significance (Dec 15, 2022)
14-24214337-G-A		not specified	Uncertain significance (Jun 28, 2023)
14-24214577-T-C		not specified	Uncertain significance (Jan 31, 2024)
14-24215571-G-A		not specified	Uncertain significance (Oct 21, 2021)
14-24215628-C-A		not specified	Uncertain significance (Jul 08, 2022)
14-24215636-C-T		not specified	Uncertain significance (Jun 22, 2023)
14-24215924-T-C		not specified	Uncertain significance (Dec 07, 2021)
14-24215951-G-C		not specified	Uncertain significance (Jun 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MDP1	protein_coding	protein_coding	ENST00000288087	6	2134

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000193	0.478	125715	0	32	125747	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.528	109	94.6	1.15	0.00000477	1158
Missense in Polyphen		41	32.311	1.2689		426
Synonymous	-0.978	44	36.5	1.21	0.00000187	339
Loss of Function	0.525	8	9.77	0.819	4.58e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000448	0.000448
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000114	0.000114
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Magnesium-dependent phosphatase which may act as a tyrosine phosphatase. {ECO:0000250}.

Intolerance Scores

• loftool: 0.462
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.148
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.874

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mdp1
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: peptidyl-tyrosine dephosphorylation
• Molecular function: protein tyrosine phosphatase activity;metal ion binding