ESX1

ESX homeobox 1, the group of PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): X:104250038-104254933

Previous symbols: [ "ESX1L" ]

Links

ENSG00000123576 ∙ NCBI:80712 ∙ OMIM:300154 ∙ HGNC:14865 ∙ Uniprot:Q8N693 ∙ 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 ESX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ESX1 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				4		4
missense		1	20	6	1	28
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	20	11	1

Variants in ESX1

This is a list of pathogenic ClinVar variants found in the ESX1 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-104250244-G-A		not specified	Uncertain significance (Jan 29, 2024)
X-104250317-TGGGTGGCAGAGGCGCCATGGGCGGCCCGGGTGGCAGAGGCGCCATGGGCGGCCC-T			Likely benign (Oct 01, 2023)
X-104250355-G-C		Male infertility with azoospermia or oligozoospermia due to single gene mutation	Likely pathogenic (Sep 01, 2023)
X-104250379-AGAGGCGCCATGGGCGGCCCGGGTGGCAGAG-A			Likely benign (Aug 01, 2024)
X-104250380-G-C			Likely benign (Apr 01, 2023)
X-104250394-G-T		not specified	Uncertain significance (Jan 09, 2024)
X-104250448-G-T		not specified	Uncertain significance (Jun 27, 2022)
X-104250461-C-G		not specified	Uncertain significance (Apr 01, 2024)
X-104250463-C-T		not specified	Uncertain significance (Oct 03, 2022)
X-104250490-G-C			Benign (May 30, 2017)
X-104250506-C-A		not specified	Uncertain significance (May 28, 2024)
X-104250529-G-A		not specified	Uncertain significance (Sep 28, 2022)
X-104250547-G-A		not specified	Likely benign (Mar 01, 2023)
X-104250548-C-T		not specified	Uncertain significance (Dec 21, 2023)
X-104250560-A-C		not specified	Likely benign (Nov 01, 2023)
X-104250580-C-G		not specified	Conflicting classifications of pathogenicity (Dec 01, 2023)
X-104250582-T-C			Likely benign (Dec 01, 2023)
X-104250584-G-A			Likely benign (Aug 01, 2023)
X-104250585-C-G			Likely benign (Aug 01, 2023)
X-104250619-G-A		not specified	Uncertain significance (Jan 30, 2024)
X-104250763-A-G		not specified	Uncertain significance (May 05, 2023)
X-104250848-G-T		not specified	Uncertain significance (Oct 27, 2023)
X-104252793-T-C		not specified	Uncertain significance (Feb 06, 2024)
X-104252799-G-C		not specified	Uncertain significance (Jun 16, 2024)
X-104254165-G-C		not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ESX1	protein_coding	protein_coding	ENST00000372588	4	4896

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.527	0.459	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0380	157	156	1.01	0.0000116	2580
Missense in Polyphen		15	16.932	0.88589		254
Synonymous	-2.80	95	66.1	1.44	0.00000541	897
Loss of Function	1.96	1	6.33	0.158	4.04e-7	102

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May coordinately regulate cell cycle progression and transcription during spermatogenesis. Inhibits degradation of polyubiquitinated cyclin A and cyclin B1 and thereby arrests the cell cycle at early M phase. ESXR1-N acts as a transcriptional repressor. Binds to the sequence 5'-TAATGTTATTA-3' which is present within the first intron of the KRAS gene and inhibits its expression. ESXR1-C has the ability to inhibit cyclin turnover. {ECO:0000269|PubMed:15235584, ECO:0000269|PubMed:15897875}.
• Pathway: Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0957

Intolerance Scores

• loftool: 0.249
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.15

Haploinsufficiency Scores

• pHI: 0.148
• hipred: N
• hipred_score: 0.269

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00000366

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Esx1
• Phenotype: embryo 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); growth/size/body region phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;negative regulation of transcription, DNA-templated;regulation of cell cycle
• Cellular component: nucleus;cytoplasm;nuclear speck
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;sequence-specific DNA binding