PM20D1

peptidase M20 domain containing 1, the group of M20 metallopeptidases

Basic information

Region (hg38): 1:205828024-205850132

Links

ENSG00000162877 ∙ NCBI:148811 ∙ OMIM:617124 ∙ HGNC:26518 ∙ Uniprot:Q6GTS8 ∙ 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 PM20D1 gene.

• Inborn genetic diseases (27 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PM20D1 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		1
missense			24	4	2	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	5	2

Variants in PM20D1

This is a list of pathogenic ClinVar variants found in the PM20D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-205828670-G-T		not specified	Uncertain significance (Dec 01, 2022)
1-205828682-A-C		not specified	Uncertain significance (Dec 17, 2023)
1-205828730-T-G		not specified	Uncertain significance (Jul 12, 2023)
1-205830281-G-A		not specified	Uncertain significance (Oct 13, 2021)
1-205830326-T-A		not specified	Uncertain significance (Oct 14, 2021)
1-205830370-A-G		not specified	Uncertain significance (Sep 14, 2023)
1-205832621-G-A		not specified	Uncertain significance (Feb 06, 2023)
1-205832628-C-T			Benign (Feb 26, 2018)
1-205832637-C-T		not specified	Likely benign (Oct 20, 2021)
1-205832645-C-T		not specified	Uncertain significance (Dec 21, 2023)
1-205832678-G-A		not specified	Uncertain significance (Feb 16, 2023)
1-205832688-C-T		not specified	Likely benign (Aug 30, 2021)
1-205832691-G-T		not specified	Uncertain significance (Feb 21, 2024)
1-205832744-A-G			Benign (Jan 11, 2019)
1-205840281-G-A		not specified	Uncertain significance (Sep 21, 2023)
1-205840319-T-C		not specified	Uncertain significance (Mar 06, 2023)
1-205841842-G-T		not specified	Uncertain significance (Aug 01, 2022)
1-205843670-C-T		not specified	Uncertain significance (Mar 17, 2023)
1-205843694-A-G		not specified	Uncertain significance (Sep 16, 2021)
1-205843719-A-C		not specified	Uncertain significance (Aug 15, 2023)
1-205843751-A-G			Likely benign (Jun 05, 2018)
1-205844091-C-T		not specified	Uncertain significance (Nov 15, 2021)
1-205844097-G-A		not specified	Uncertain significance (Sep 13, 2022)
1-205844124-C-T		not specified	Uncertain significance (Dec 02, 2022)
1-205844168-C-T		not specified	Uncertain significance (Jun 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PM20D1	protein_coding	protein_coding	ENST00000367136	13	22111

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.90e-18	0.00347	125637	1	110	125748	0.000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.417	266	286	0.931	0.0000158	3265
Missense in Polyphen		73	74.372	0.98155		914
Synonymous	-0.0747	120	119	1.01	0.00000731	1012
Loss of Function	-0.0642	27	26.6	1.01	0.00000148	279

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00117	0.00117
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000544	0.000489
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000370	0.000369
Middle Eastern	0.000544	0.000489
South Asian	0.000926	0.000915
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Bidirectional N-fatty-acyl amino acid synthase/hydrolase that regulates the production of N-fatty-acyl amino acids. These metabolites are endogenous chemical uncouplers of mitochondrial respiration. In an UCP1-independent manner, maybe through interaction with mitochondrial transporters, they promote proton leakage into the mitochondrial matrix. Thereby, this secreted protein may indirectly regulate the bodily dissipation of chemical energy as heat through thermogenic respiration. {ECO:0000269|PubMed:27374330}.

Recessive Scores

• pRec: 0.0669

Intolerance Scores

• loftool: 0.944
• rvis_EVS: 1.33
• rvis_percentile_EVS: 94.22

Haploinsufficiency Scores

• pHI: 0.0430
• hipred: N
• hipred_score: 0.227

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.233

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Pm20d1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism 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)

Gene ontology

• Biological process: proteolysis;cellular amino acid metabolic process;nitrogen compound metabolic process;amide biosynthetic process;cellular amide catabolic process;cellular lipid metabolic process;energy homeostasis;negative regulation of neuron death;adaptive thermogenesis;regulation of oxidative phosphorylation uncoupler activity
• Cellular component: extracellular exosome
• Molecular function: peptidase activity;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides;lyase activity;metal ion binding