GSX1

GS homeobox 1, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 13:27792482-27794768

Previous symbols: [ "GSH1" ]

Links

ENSG00000169840 ∙ NCBI:219409 ∙ OMIM:616542 ∙ HGNC:20374 ∙ Uniprot:Q9H4S2 ∙ 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 GSX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GSX1 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			13	1	1	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	2

Variants in GSX1

This is a list of pathogenic ClinVar variants found in the GSX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-27792706-C-A		not specified	Uncertain significance (Jan 06, 2023)
13-27792732-G-C		not specified	Uncertain significance (Jun 16, 2023)
13-27792772-C-T		not specified	Uncertain significance (Apr 07, 2023)
13-27792790-C-A		not specified	Uncertain significance (Jan 23, 2024)
13-27792838-C-G		not specified	Uncertain significance (Mar 19, 2024)
13-27792856-T-C		not specified	Uncertain significance (Dec 09, 2023)
13-27792878-C-A		not specified	Uncertain significance (May 11, 2022)
13-27792892-C-A		not specified	Uncertain significance (Feb 22, 2023)
13-27792896-G-A		not specified	Uncertain significance (Jun 24, 2022)
13-27792898-C-A		not specified	Uncertain significance (May 13, 2024)
13-27792901-C-T		not specified	Uncertain significance (Oct 06, 2021)
13-27792925-C-T		not specified	Uncertain significance (Jul 13, 2022)
13-27792965-A-G		not specified	Uncertain significance (Oct 13, 2021)
13-27792966-C-A		not specified	Uncertain significance (Nov 30, 2022)
13-27792966-C-G		not specified	Uncertain significance (Jan 18, 2022)
13-27793015-G-A		not specified	Likely benign (Feb 06, 2024)
13-27793053-G-A			Benign (Aug 11, 2018)
13-27793054-A-T			Benign (Aug 11, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GSX1	protein_coding	protein_coding	ENST00000302945	2	2126

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0440	0.859	122503	0	3	122506	0.0000122

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.498	117	133	0.879	0.00000610	1646
Missense in Polyphen		21	41.354	0.50781		497
Synonymous	-0.597	66	60.1	1.10	0.00000288	579
Loss of Function	1.36	3	6.83	0.439	2.97e-7	79

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000545
Finnish	0.00	0.00
European (Non-Finnish)	0.00000910	0.00000906
Middle Eastern	0.0000547	0.0000545
South Asian	0.0000398	0.0000339
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable transcription factor that binds to the DNA sequence 5'-GC[TA][AC]ATTA[GA]-3'. Activates the transcription of the GHRH gene. Plays an important role in pituitary development.

Recessive Scores

• pRec: 0.155

Haploinsufficiency Scores

• pHI: 0.220
• hipred: Y
• hipred_score: 0.752
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.418

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gsx1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system 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); hematopoietic system phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; immune system phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; craniofacial phenotype

Gene ontology

• Biological process: spinal cord association neuron differentiation;hypothalamus development;adenohypophysis development;positive regulation of transcription by RNA polymerase II;neuron fate commitment
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;sequence-specific DNA binding