PYM1

PYM homolog 1, exon junction complex associated factor

Basic information

Region (hg38): 12:55901413-55932618

Previous symbols: [ "WIBG" ]

Links

ENSG00000170473 ∙ NCBI:84305 ∙ OMIM:619753 ∙ HGNC:30258 ∙ Uniprot:Q9BRP8 ∙ 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 PYM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PYM1 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in PYM1

This is a list of pathogenic ClinVar variants found in the PYM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-55902071-G-A		not specified	Uncertain significance (Mar 28, 2023)
12-55902092-C-T		not specified	Uncertain significance (Feb 03, 2022)
12-55902155-C-G		not specified	Uncertain significance (Mar 29, 2023)
12-55902257-T-C		not specified	Uncertain significance (Aug 12, 2021)
12-55902269-G-A		not specified	Uncertain significance (Jul 08, 2022)
12-55902279-G-A		not specified	Uncertain significance (Dec 14, 2024)
12-55902317-G-A		not specified	Uncertain significance (Dec 14, 2021)
12-55903448-C-T		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PYM1	protein_coding	protein_coding	ENST00000408946	3	31206

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0219	0.916	124793	0	2	124795	0.00000801

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	72	114	0.632	0.00000671	1301
Missense in Polyphen		7	29.656	0.23604		349
Synonymous	-0.692	51	45.1	1.13	0.00000235	418
Loss of Function	1.59	4	9.20	0.435	5.65e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000884	0.00000883
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Key regulator of the exon junction complex (EJC), a multiprotein complex that associates immediately upstream of the exon-exon junction on mRNAs and serves as a positional landmark for the intron exon structure of genes and directs post- transcriptional processes in the cytoplasm such as mRNA export, nonsense-mediated mRNA decay (NMD) or translation. Acts as an EJC disassembly factor, allowing translation-dependent EJC removal and recycling by disrupting mature EJC from spliced mRNAs. Its association with the 40S ribosomal subunit probably prevents a translation-independent disassembly of the EJC from spliced mRNAs, by restricting its activity to mRNAs that have been translated. Interferes with NMD and enhances translation of spliced mRNAs, probably by antagonizing EJC functions. May bind RNA; the relevance of RNA-binding remains unclear in vivo, RNA-binding was detected by PubMed:14968132, while PubMed:19410547 did not detect RNA-binding activity independently of the EJC. {ECO:0000269|PubMed:18026120, ECO:0000269|PubMed:19410547}.
• Pathway: mRNA surveillance pathway - Homo sapiens (human);RNA transport - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.155
• hipred: Y
• hipred_score: 0.550
• ghis: 0.589

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Pym1

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;positive regulation of translation;exon-exon junction complex disassembly
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;cytosol;cell junction;exon-exon junction complex
• Molecular function: RNA binding;protein binding;ribosome binding