PM20D2

peptidase M20 domain containing 2, the group of M20 metallopeptidases

Basic information

Region (hg38): 6:89146055-89165565

Previous symbols: [ "ACY1L2" ]

Links

ENSG00000146281 ∙ NCBI:135293 ∙ OMIM:615913 ∙ HGNC:21408 ∙ Uniprot:Q8IYS1 ∙ 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 PM20D2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PM20D2 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			32	1		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	1	0

Variants in PM20D2

This is a list of pathogenic ClinVar variants found in the PM20D2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-89146151-C-T		not specified	Uncertain significance (Mar 25, 2024)
6-89146170-T-C		not specified	Uncertain significance (Jul 09, 2021)
6-89146173-A-C		not specified	Uncertain significance (Jun 12, 2023)
6-89146197-C-T		not specified	Uncertain significance (Apr 09, 2024)
6-89146200-A-T		not specified	Uncertain significance (Sep 28, 2022)
6-89146220-C-T		not specified	Uncertain significance (Jan 09, 2024)
6-89146295-C-G		not specified	Uncertain significance (Dec 16, 2023)
6-89146296-T-A		not specified	Uncertain significance (Nov 08, 2021)
6-89146358-G-A		not specified	Uncertain significance (Sep 27, 2022)
6-89146401-C-G		not specified	Uncertain significance (Feb 27, 2024)
6-89146433-C-G		not specified	Uncertain significance (Feb 03, 2022)
6-89146440-C-G		not specified	Uncertain significance (Sep 16, 2021)
6-89146475-C-G		not specified	Uncertain significance (Apr 04, 2024)
6-89146475-C-T		not specified	Uncertain significance (Jun 09, 2022)
6-89146490-G-T		not specified	Uncertain significance (Apr 24, 2024)
6-89146505-G-C		not specified	Uncertain significance (Aug 17, 2022)
6-89146532-G-T		not specified	Uncertain significance (May 29, 2024)
6-89146544-G-T		not specified	Uncertain significance (Nov 29, 2023)
6-89146575-T-C		not specified	Uncertain significance (Aug 13, 2021)
6-89146601-C-A		not specified	Uncertain significance (Jul 19, 2023)
6-89146601-C-T		not specified	Uncertain significance (Nov 23, 2022)
6-89146604-G-T		not specified	Uncertain significance (Feb 02, 2022)
6-89149272-T-C		not specified	Uncertain significance (Oct 05, 2023)
6-89149348-T-A		not specified	Uncertain significance (Jun 24, 2022)
6-89149377-A-G		not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PM20D2	protein_coding	protein_coding	ENST00000275072	7	19516

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000683	0.916	125712	0	34	125746	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.979	171	211	0.810	0.00000995	2761
Missense in Polyphen		38	60.19	0.63134		729
Synonymous	0.915	74	84.7	0.874	0.00000421	887
Loss of Function	1.59	9	15.8	0.569	6.65e-7	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000510	0.000510
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000714	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.000331	0.000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Haploinsufficiency Scores

• pHI: 0.114
• hipred: N
• hipred_score: 0.248
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.239

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pm20d2

Gene ontology

• Biological process: proteolysis;regulation of cellular protein metabolic process;folic acid catabolic process
• Cellular component: nucleoplasm;cytoplasm
• Molecular function: dipeptidase activity;para-aminobenzoyl-glutamate hydrolase activity