MPND

MPN domain containing, the group of JAMM/MPN+ metallopeptidase family

Basic information

Region (hg38): 19:4343527-4360086

Links

ENSG00000008382 ∙ NCBI:84954 ∙ ∙ HGNC:25934 ∙ Uniprot:Q8N594 ∙ 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 MPND gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MPND 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			42	3		45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	3	0

Variants in MPND

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

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

Position	Type	Phenotype	Significance	ClinVar
19-4343738-C-T		not specified	Uncertain significance (Oct 14, 2023)
19-4343741-G-A		not specified	Uncertain significance (Dec 14, 2023)
19-4343769-C-G		not specified	Uncertain significance (Jul 09, 2021)
19-4343792-A-C		not specified	Uncertain significance (Dec 20, 2022)
19-4343804-C-T		not specified	Uncertain significance (Sep 16, 2021)
19-4343845-G-C		not specified	Uncertain significance (Mar 17, 2023)
19-4343951-C-A		not specified	Uncertain significance (Apr 05, 2023)
19-4343972-G-A		not specified	Uncertain significance (Oct 25, 2022)
19-4345763-G-A		not specified	Uncertain significance (Dec 26, 2023)
19-4345782-G-A		not specified	Uncertain significance (Jan 03, 2024)
19-4345820-C-T		not specified	Uncertain significance (Aug 30, 2021)
19-4345823-A-T		not specified	Uncertain significance (Jun 29, 2023)
19-4345878-G-A		not specified	Uncertain significance (Mar 01, 2024)
19-4345937-C-T		not specified	Uncertain significance (Aug 21, 2023)
19-4345940-C-T		not specified	Uncertain significance (Jan 26, 2023)
19-4345941-G-A		not specified	Uncertain significance (Feb 28, 2023)
19-4345976-G-T		not specified	Uncertain significance (May 23, 2024)
19-4352946-A-G		not specified	Uncertain significance (Jan 23, 2023)
19-4352954-G-A		not specified	Uncertain significance (Mar 19, 2024)
19-4352994-C-A		not specified	Uncertain significance (Nov 03, 2022)
19-4354066-G-T		not specified	Uncertain significance (May 25, 2022)
19-4354073-C-G		not specified	Likely benign (Jun 29, 2023)
19-4354096-G-A		not specified	Uncertain significance (Jan 26, 2023)
19-4354119-G-A		not specified	Uncertain significance (Jun 13, 2024)
19-4354352-T-A		not specified	Uncertain significance (Jul 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MPND	protein_coding	protein_coding	ENST00000262966	12	16560

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000527	0.972	124732	0	40	124772	0.000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.310	214	227	0.942	0.0000140	2979
Missense in Polyphen		77	81.307	0.94703		872
Synonymous	-0.503	110	103	1.06	0.00000699	961
Loss of Function	1.97	10	19.4	0.516	8.25e-7	269

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000261	0.000261
Ashkenazi Jewish	0.00	0.00
East Asian	0.00112	0.00111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000800	0.0000795
Middle Eastern	0.00112	0.00111
South Asian	0.0000654	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable protease. {ECO:0000250}.

Recessive Scores

• pRec: 0.0965

Intolerance Scores

• loftool: 0.226
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.96

Haploinsufficiency Scores

• pHI: 0.0848
• hipred: N
• hipred_score: 0.267
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.895

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mpnd

Zebrafish Information Network

• Gene name: mpnd
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: proteolysis
• Molecular function: metallopeptidase activity;metal ion binding