JMY

protein-coding

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

Gene summary

Enables microtubule binding activity. Involved in cellular response to starvation. Located in autophagosome membrane; cell leading edge; and cytoplasmic vesicle. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_152405.5

Inheritance

—

ClinVar variants

U:145B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr5:79,236,131-79,327,211

External References & Databases

Ensembl (ENSG00000152409)

Transcript & Mutation Effects

hg38 • Region Span ~91.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to JMY variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 141

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152405.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar	2 clinvar	5
missense			141 clinvar	3 clinvar	2 clinvar	146
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	145	4	4	153

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152405.5	RefSeq	NP_689618.4	10	MANE Select
ENST00000396137.5	Ensembl	ENSP00000379441.4	10	MANE Select
ENST00000850851.1	Ensembl	ENSP00000520940.1	10	Standard
ENST00000850851.2	Ensembl	ENSP00000520940.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription
Regulation of TP53 Activity through Methylation
Regulation of TP53 Activity

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

Molecular Function

transcription coactivator activity
actin binding
protein binding
Arp2/3 complex binding

Cellular Component

nucleus
nucleoplasm
cytoplasm
cytoskeleton
cell leading edge

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000396137
Coding exons: 10
Length: 91027
Individuals with no LoFs: 124756
Homozygous LoFs: 0
Heterozygous LoFs: 43
Defined: 124799
p: 0.000172

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.71	392	499	0.785	0.0000250	6343
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00033	0.00032	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000056	0.000056	rare
Finnish	0.00069	0.00065	rare
European (Non-Finnish)	0.000083	0.000079	rare
South Asian	0.00014	0.00013	rare
Other	0.00053	0.00049	rare

dbNSFP Gene Annotations

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}.;

Intolerance Scores

LoFtool: 0.222
RVIS EVS: 0.89
RVIS percentile EVS: 89.24

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.503

Gene Damage Prediction

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