MAP4K3

mitogen-activated protein kinase kinase kinase kinase 3, the group of Mitogen-activated protein kinase kinase kinase kinases

Basic information

Region (hg38): 2:39249266-39437301

Previous symbols: [ "RAB8IPL1" ]

Links

ENSG00000011566 ∙ NCBI:8491 ∙ OMIM:604921 ∙ HGNC:6865 ∙ Uniprot:Q8IVH8 ∙ 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 MAP4K3 gene.

• not_specified (89 variants)
• not_provided (4 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
• Ependymoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAP4K3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003618.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			87	3		90
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)				1		1
Total	0	0	87	6	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAP4K3	protein_coding	protein_coding	ENST00000263881	34	188047

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.110	0.890	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.45	374	461	0.811	0.0000221	5869
Missense in Polyphen		147	240.91	0.61019		3070
Synonymous	-1.11	173	155	1.11	0.00000772	1591
Loss of Function	5.54	15	62.1	0.242	0.00000296	787

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000154	0.000152
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000153	0.000139
European (Non-Finnish)	0.000163	0.000158
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000343	0.0000327
Other	0.000183	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the response to environmental stress. Appears to act upstream of the JUN N-terminal pathway. {ECO:0000269|PubMed:9275185}.
• Pathway: MAPK signaling pathway - Homo sapiens (human);EGF-Core;MAPK Signaling Pathway;Angiopoietin Like Protein 8 Regulatory Pathway;Insulin Signaling;mapkinase signaling pathway;IL-7 signaling;JAK STAT pathway and regulation;EPO signaling;VEGF;TNF receptor signaling pathway (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.662
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.73

Haploinsufficiency Scores

• pHI: 0.562
• hipred: Y
• hipred_score: 0.706
• ghis: 0.589

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.923

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Map4k3
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: activation of MAPKKK activity;protein phosphorylation;JNK cascade;response to UV;signal transduction by protein phosphorylation;stress-activated protein kinase signaling cascade;activation of protein kinase activity;response to tumor necrosis factor;intracellular signal transduction
• Cellular component: cytoplasm
• Molecular function: protein kinase activity;protein serine/threonine kinase activity;protein binding;ATP binding;MAP kinase kinase kinase kinase activity