JMY

junction mediating and regulatory protein, p53 cofactor, the group of Wiskott-Aldrich Syndrome protein family

Basic information

Region (hg38): 5:79236131-79327211

Links

ENSG00000152409 ∙ NCBI:133746 ∙ OMIM:604279 ∙ HGNC:28916 ∙ Uniprot:Q8N9B5 ∙ 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 JMY gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JMY 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	2	3
missense			52	1	2	55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	2	4

Variants in JMY

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

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

Position	Type	Phenotype	Significance	ClinVar
5-79236763-T-C		not specified	Uncertain significance (Oct 29, 2021)
5-79236768-G-T		not specified	Uncertain significance (Dec 17, 2023)
5-79236861-G-A		not specified	Uncertain significance (May 04, 2023)
5-79236865-G-A		not specified	Uncertain significance (Apr 19, 2023)
5-79236987-G-A		not specified	Uncertain significance (Apr 26, 2024)
5-79236994-C-G		not specified	Uncertain significance (Aug 12, 2021)
5-79236999-C-T		not specified	Uncertain significance (Nov 18, 2023)
5-79237008-C-T		not specified	Uncertain significance (Mar 31, 2024)
5-79237051-A-G		not specified	Uncertain significance (Jul 12, 2023)
5-79237089-A-G		not specified	Uncertain significance (Apr 10, 2023)
5-79237093-C-T		not specified	Uncertain significance (Aug 13, 2021)
5-79237102-G-C		not specified	Uncertain significance (Nov 14, 2023)
5-79237106-G-C		not specified	Uncertain significance (Mar 25, 2022)
5-79237134-G-T		not specified	Uncertain significance (Oct 12, 2021)
5-79237138-C-T		not specified	Uncertain significance (Jul 19, 2023)
5-79237155-C-G		not specified	Uncertain significance (Jan 16, 2024)
5-79237171-A-C		not specified	Uncertain significance (Mar 13, 2023)
5-79237231-A-T		not specified	Uncertain significance (Sep 30, 2021)
5-79237427-C-A		not specified	Uncertain significance (Jan 23, 2024)
5-79237650-G-T		not specified	Uncertain significance (Mar 22, 2023)
5-79237665-A-C			Likely benign (Jun 15, 2018)
5-79277927-G-T		not specified	Uncertain significance (Jun 06, 2023)
5-79277951-T-C			Benign (Jun 21, 2018)
5-79277952-C-G		not specified	Uncertain significance (Aug 21, 2023)
5-79277955-G-A			Benign (Jun 15, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JMY	protein_coding	protein_coding	ENST00000396137	10	91027

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.960	0.0397	124756	0	43	124799	0.000172

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.71	392	499	0.785	0.0000250	6343
Missense in Polyphen		150	230.58	0.65052		3013
Synonymous	-0.496	202	193	1.05	0.00000941	1975
Loss of Function	5.14	8	45.3	0.176	0.00000257	525

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000327	0.000327
Ashkenazi Jewish	0.0000994	0.0000993
East Asian	0.0000556	0.0000556
Finnish	0.000692	0.000650
European (Non-Finnish)	0.0000826	0.0000794
Middle Eastern	0.0000556	0.0000556
South Asian	0.000137	0.000131
Other	0.000527	0.000495

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts both as a nuclear p53/TP53-cofactor and a cytoplasmic regulator of actin dynamics depending on conditions. In nucleus, acts as a cofactor that increases p53/TP53 response via its interaction with p300/EP300. Increases p53/TP53-dependent transcription and apoptosis, suggesting an important role in p53/TP53 stress response such as DNA damage. In cytoplasm, acts as a nucleation-promoting factor for both branched and unbranched actin filaments. Activates the Arp2/3 complex to induce branched actin filament networks. Also catalyzes actin polymerization in the absence of Arp2/3, creating unbranched filaments. Contributes to cell motility by controlling actin dynamics. May promote the rapid formation of a branched actin network by first nucleating new mother filaments and then activating Arp2/3 to branch off these filaments. The p53/TP53-cofactor and actin activator activities are regulated via its subcellular location (By similarity). {ECO:0000250}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Regulation of TP53 Activity through Methylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Direct p53 effectors (Consensus)

Intolerance Scores

• loftool: 0.222
• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.24

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.726
• ghis: 0.436

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.503

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Jmy

Gene ontology

• Biological process: DNA repair;regulation of transcription by RNA polymerase II;cell cycle arrest;Arp2/3 complex-mediated actin nucleation;positive regulation of apoptotic process;positive regulation of DNA-binding transcription factor activity;'de novo' actin filament nucleation;actin polymerization-dependent cell motility;intrinsic apoptotic signaling pathway by p53 class mediator;regulation of signal transduction by p53 class mediator;positive regulation of nucleic acid-templated transcription
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytoskeleton;cell leading edge
• Molecular function: transcription coactivator activity;actin binding;protein binding;Arp2/3 complex binding