ECSIT

ECSIT signaling integrator, the group of Mitochondrial complex I assembly complex

Basic information

Region (hg38): 19:11505929-11529172

Links

ENSG00000130159 ∙ NCBI:51295 ∙ OMIM:608388 ∙ HGNC:29548 ∙ Uniprot:Q9BQ95 ∙ 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 ECSIT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ECSIT 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		1
missense			29	2		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	29	3	0

Variants in ECSIT

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

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

Position	Type	Phenotype	Significance	ClinVar
19-11506205-T-G			Likely benign (Mar 01, 2023)
19-11507511-C-T		not specified	Uncertain significance (Jan 24, 2025)
19-11507515-C-T		not specified	Uncertain significance (Dec 12, 2023)
19-11507549-G-A		not specified	Likely benign (Jan 24, 2025)
19-11507562-C-T		not specified	Uncertain significance (Dec 22, 2023)
19-11507994-C-T		not specified	Uncertain significance (Oct 16, 2024)
19-11508029-G-A		not specified	Uncertain significance (Feb 28, 2023)
19-11508040-C-G		not specified	Uncertain significance (Dec 20, 2023)
19-11513050-G-A			Benign (Oct 01, 2024)
19-11513105-C-T		not specified	Uncertain significance (Jun 17, 2024)
19-11513144-C-T		not specified	Uncertain significance (Aug 04, 2021)
19-11513184-A-C		not specified	Uncertain significance (Mar 07, 2024)
19-11513216-G-A		not specified	Uncertain significance (Jan 29, 2024)
19-11513241-G-C		not specified	Uncertain significance (May 14, 2024)
19-11513833-A-G		not specified	Uncertain significance (Aug 04, 2021)
19-11513839-C-T		not specified	Uncertain significance (Nov 14, 2024)
19-11513873-G-A		not specified	Uncertain significance (Nov 18, 2022)
19-11513894-G-C		not specified	Uncertain significance (May 02, 2024)
19-11513948-G-A		not specified	Uncertain significance (Jun 16, 2024)
19-11513956-C-T		not specified	Uncertain significance (Jun 19, 2024)
19-11513966-G-A		not specified	Uncertain significance (Aug 30, 2021)
19-11513975-G-A		not specified	Uncertain significance (Sep 30, 2024)
19-11514008-G-A		not specified	Uncertain significance (Apr 30, 2024)
19-11514017-C-T		not specified	Uncertain significance (Apr 24, 2023)
19-11514028-G-A		not specified	Uncertain significance (Sep 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ECSIT	protein_coding	protein_coding	ENST00000270517	7	23259

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000676	0.907	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.184	262	271	0.968	0.0000184	2807
Missense in Polyphen		68	75.873	0.89623		833
Synonymous	1.20	97	113	0.857	0.00000731	882
Loss of Function	1.61	11	18.5	0.595	9.63e-7	190

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000326	0.000326
South Asian	0.000294	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adapter protein of the Toll-like and IL-1 receptor signaling pathway that is involved in the activation of NF-kappa-B via MAP3K1. Promotes proteolytic activation of MAP3K1. Involved in the BMP signaling pathway. Required for normal embryonic development (By similarity). {ECO:0000250}.
• Pathway: MAPK signaling pathway - Homo sapiens (human);IL-1 signaling pathway;Simplified Interaction Map Between LOXL4 and Oxidative Stress Pathway;MAPK Signaling Pathway;TLR NFkB;Toll Like Receptor 7/8 (TLR7/8) Cascade;signal transduction through il1r;toll-like receptor pathway;Toll Like Receptor 9 (TLR9) Cascade;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;Toll Like Receptor 5 (TLR5) Cascade;Toll-Like Receptors Cascades;Respiratory electron transport;The citric acid (TCA) cycle and respiratory electron transport;Innate Immune System;Immune System;Metabolism;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;MyD88 dependent cascade initiated on endosome;TLR ECSIT MEKK1 JNK;TLR ECSIT MEKK1 p38;Complex I biogenesis;Toll Like Receptor 4 (TLR4) Cascade;Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.751
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.33

Haploinsufficiency Scores

• pHI: 0.162
• hipred: Y
• hipred_score: 0.504
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.873

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ecsit
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); embryo phenotype; growth/size/body region phenotype; cellular phenotype; muscle phenotype

Gene ontology

• Biological process: mitochondrial respiratory chain complex I assembly;innate immune response;regulation of oxidoreductase activity;oxidation-reduction process
• Cellular component: nucleus;nucleoplasm;cytoplasm;mitochondrion;mitochondrial inner membrane;cytosol
• Molecular function: protein binding;oxidoreductase activity, acting on NAD(P)H