MAP4K1

mitogen-activated protein kinase kinase kinase kinase 1, the group of Mitogen-activated protein kinase kinase kinase kinases

Basic information

Region (hg38): 19:38587641-38618882

Links

ENSG00000104814 ∙ NCBI:11184 ∙ OMIM:601983 ∙ HGNC:6863 ∙ Uniprot:Q92918 ∙ 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 MAP4K1 gene.

• not_specified (70 variants)
• not_provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAP4K1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001042600.3. 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				4		4
missense			67	2		69
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	67	6	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAP4K1	protein_coding	protein_coding	ENST00000591517	32	31242

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.989	0.0108	124783	0	30	124813	0.000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.13	279	470	0.594	0.0000277	5316
Missense in Polyphen		75	180.91	0.41456		2037
Synonymous	0.0775	190	191	0.993	0.0000118	1688
Loss of Function	5.62	9	53.3	0.169	0.00000279	606

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000978	0.000961
Ashkenazi Jewish	0.000100	0.0000993
East Asian	0.00	0.00
Finnish	0.000186	0.000186
European (Non-Finnish)	0.0000707	0.0000618
Middle Eastern	0.00	0.00
South Asian	0.0000332	0.0000327
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine/threonine-protein kinase, which may play a role in the response to environmental stress. Appears to act upstream of the JUN N-terminal pathway. May play a role in hematopoietic lineage decisions and growth regulation. Able to autophosphorylate. {ECO:0000269|PubMed:24362026, ECO:0000269|PubMed:8824585}.
• Pathway: MAPK signaling pathway - Homo sapiens (human);EGF-Core;Androgen Receptor Network in Prostate Cancer;B Cell Receptor Signaling Pathway;Cardiac Hypertrophic Response;Signaling of Hepatocyte Growth Factor Receptor;TGF-beta Signaling Pathway;MAPK Signaling Pathway;Angiopoietin Like Protein 8 Regulatory Pathway;EGF-EGFR Signaling Pathway;Insulin Signaling;T-Cell antigen Receptor (TCR) Signaling Pathway;mapkinase signaling pathway;TCR;TGF_beta_Receptor;BCR signaling pathway;Signaling events mediated by Stem cell factor receptor (c-Kit);JNK signaling in the CD4+ TCR pathway;TCR signaling in naïve CD4+ T cells (Consensus)

Intolerance Scores

• loftool: 0.542
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.73

Haploinsufficiency Scores

• pHI: 0.745
• hipred: Y
• hipred_score: 0.694
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.854

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Map4k1
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: activation of MAPKKK activity;protein phosphorylation;activation of JUN kinase activity;cell population proliferation;peptidyl-serine phosphorylation;signal transduction by protein phosphorylation;stress-activated protein kinase signaling cascade;activation of protein kinase activity;protein autophosphorylation;cellular response to phorbol 13-acetate 12-myristate
• Cellular component: cytoplasm;membrane
• Molecular function: protein kinase activity;protein serine/threonine kinase activity;protein binding;ATP binding;MAP kinase kinase kinase kinase activity