MAP3K15

mitogen-activated protein kinase kinase kinase 15, the group of Mitogen-activated protein kinase kinase kinases

Basic information

Region (hg38): X:19360056-19515508

Links

ENSG00000180815 ∙ NCBI:389840 ∙ OMIM:300820 ∙ HGNC:31689 ∙ Uniprot:Q6ZN16 ∙ 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 MAP3K15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAP3K15 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				14	4	18
missense			85	7	9	101
nonsense			1			1
start loss						0
frameshift			2	1		3
inframe indel						0
splice donor/acceptor (+/-2bp)			1	1		2
splice region			1	3	2	6
non coding			8	3	17	28
Total	0	0	97	26	30

Variants in MAP3K15

This is a list of pathogenic ClinVar variants found in the MAP3K15 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-19360085-C-T		Pyruvate dehydrogenase E1-alpha deficiency	Conflicting classifications of pathogenicity (Dec 01, 2022)
X-19360178-C-G		Pyruvate dehydrogenase E1-alpha deficiency	Benign (Jan 13, 2018)
X-19360202-A-G		Pyruvate dehydrogenase E1-alpha deficiency	Conflicting classifications of pathogenicity (Jun 01, 2023)
X-19360228-T-C		Pyruvate dehydrogenase E1-alpha deficiency	Conflicting classifications of pathogenicity (Nov 01, 2022)
X-19360267-G-T		Pyruvate dehydrogenase E1-alpha deficiency	Benign (Jan 12, 2018)
X-19360360-G-A		Pyruvate dehydrogenase E1-alpha deficiency	Benign (Jan 12, 2018)
X-19360381-C-T		Pyruvate dehydrogenase E1-alpha deficiency	Benign (Jan 13, 2018)
X-19360382-G-A		Pyruvate dehydrogenase E1-alpha deficiency	Uncertain significance (Jan 13, 2018)
X-19360497-A-G		Pyruvate dehydrogenase E1-alpha deficiency	Benign (Jan 13, 2018)
X-19360510-A-G		Pyruvate dehydrogenase E1-alpha deficiency	Benign (Jan 13, 2018)
X-19360517-G-A		Pyruvate dehydrogenase E1-alpha deficiency	Benign (Jan 12, 2018)
X-19360666-C-A		Pyruvate dehydrogenase E1-alpha deficiency	Benign (Jan 12, 2018)
X-19360712-G-A		Pyruvate dehydrogenase E1-alpha deficiency	Benign (Jan 13, 2018)
X-19360739-C-CTGAT		PDHA1-related disorder	Likely benign (Apr 16, 2019)
X-19360785-C-G		not specified	Conflicting classifications of pathogenicity (Jun 01, 2023)
X-19360844-AAC-A			Likely benign (Feb 20, 2017)
X-19360861-A-C		Pyruvate dehydrogenase E1-alpha deficiency	Benign (Jan 13, 2018)
X-19360950-G-A		Pyruvate dehydrogenase E1-alpha deficiency	Uncertain significance (Mar 30, 2018)
X-19360955-G-A			Likely benign (Jan 01, 2023)
X-19360959-G-A		Pyruvate dehydrogenase E1-alpha deficiency	Uncertain significance (Jan 13, 2018)
X-19360998-A-G		Pyruvate dehydrogenase E1-alpha deficiency	Benign (Jan 13, 2018)
X-19361000-C-T		Pyruvate dehydrogenase E1-alpha deficiency	Uncertain significance (Jan 12, 2018)
X-19361029-C-T		Pyruvate dehydrogenase E1-alpha deficiency	Uncertain significance (Mar 16, 2018)
X-19361030-G-A		Pyruvate dehydrogenase E1-alpha deficiency	Benign (Jan 13, 2018)
X-19361047-C-T		Pyruvate dehydrogenase E1-alpha deficiency	Benign (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAP3K15	protein_coding	protein_coding	ENST00000338883	29	155206

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.93e-32	0.0000125	125588	51	109	125748	0.000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.783	523	475	1.10	0.0000381	8531
Missense in Polyphen		139	147.53	0.94216		2838
Synonymous	-1.53	219	192	1.14	0.0000164	2514
Loss of Function	-0.299	47	44.8	1.05	0.00000343	801

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00104	0.000825
Ashkenazi Jewish	0.00	0.00
East Asian	0.00214	0.00158
Finnish	0.000182	0.0000924
European (Non-Finnish)	0.000803	0.000554
Middle Eastern	0.00214	0.00158
South Asian	0.00238	0.00134
Other	0.00180	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function in a signal transduction pathway that is activated by various cell stresses and leads to apoptosis. {ECO:0000269|PubMed:20362554}.

Recessive Scores

• pRec: 0.0939

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.352

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.563

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Map3k15
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); renal/urinary system phenotype; cellular phenotype

Gene ontology

• Biological process: MAPK cascade;activation of MAPKK activity
• Molecular function: protein kinase activity;MAP kinase kinase kinase activity;ATP binding;metal ion binding