GSX2

GS homeobox 2, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 4:54099523-54102498

Links

ENSG00000180613 ∙ NCBI:170825 ∙ OMIM:616253 ∙ HGNC:24959 ∙ Uniprot:Q9BZM3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• diencephalic-mesencephalic junction dysplasia syndrome 2 (Limited), mode of inheritance: Unknown
• diencephalic-mesencephalic junction dysplasia syndrome 2 (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GSX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GSX2 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	2	3
missense			22	1	1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					3	3
Total	0	0	22	2	6

Variants in GSX2

This is a list of pathogenic ClinVar variants found in the GSX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-54099937-G-A			Benign (May 12, 2021)
4-54100370-C-A		Diencephalic-mesencephalic junction dysplasia syndrome 2	no classifications from unflagged records (Mar 28, 2024)
4-54100378-A-G			Likely benign (May 01, 2023)
4-54100390-T-A		not specified	Uncertain significance (Mar 01, 2024)
4-54100462-C-G		not specified	Uncertain significance (May 09, 2023)
4-54100479-G-A			Likely benign (May 01, 2022)
4-54100500-C-T		Diencephalic-mesencephalic junction dysplasia syndrome 2	Benign (Aug 10, 2021)
4-54100529-C-A		not specified	Uncertain significance (Aug 20, 2024)
4-54100558-T-C		not specified	Uncertain significance (Mar 28, 2023)
4-54100606-A-G		not specified	Likely benign (Jan 24, 2025)
4-54100616-G-A		not specified	Uncertain significance (Aug 16, 2021)
4-54100627-G-T		not specified	Uncertain significance (Jul 12, 2022)
4-54100639-G-T		not specified	Uncertain significance (Jul 31, 2024)
4-54100663-G-A		Diencephalic-mesencephalic junction dysplasia syndrome 2	Benign (Aug 10, 2021)
4-54100687-G-T		not specified	Uncertain significance (Dec 14, 2022)
4-54100688-A-G		not specified	Uncertain significance (Sep 30, 2021)
4-54100690-G-A		not specified	Uncertain significance (Aug 07, 2024)
4-54100702-C-A		not specified	Uncertain significance (Feb 05, 2024)
4-54100714-C-A		not specified	Uncertain significance (Dec 03, 2024)
4-54100733-A-C		not specified	Uncertain significance (Dec 01, 2022)
4-54100752-T-C		Diencephalic-mesencephalic junction dysplasia syndrome 2	Benign (Aug 10, 2021)
4-54100787-C-T		not specified	Uncertain significance (Aug 20, 2024)
4-54100803-A-C		GSX2-related disorder	Likely benign (Feb 07, 2022)
4-54100825-G-A		not specified	Uncertain significance (Oct 09, 2024)
4-54100839-C-G		not specified	Uncertain significance (Jan 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GSX2	protein_coding	protein_coding	ENST00000326902	2	2983

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.257	0.718	125674	0	59	125733	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.592	143	164	0.870	0.00000746	1912
Missense in Polyphen		41	67.384	0.60845		773
Synonymous	-0.157	78	76.3	1.02	0.00000372	648
Loss of Function	1.89	2	7.62	0.262	3.33e-7	82

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00316	0.00316
Finnish	0.00	0.00
European (Non-Finnish)	0.00000886	0.00000879
Middle Eastern	0.00316	0.00316
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: During telencephalic development, causes ventralization of pallial progenitors and, depending on the developmental stage, specifies different neuronal fates. At early stages, necessary and sufficient to correctly specify the ventral lateral ganglionic eminence (LGE) and its major derivatives, the striatal projection neurons. At later stages, may specify LGE progenitors toward dorsal LGE fates, including olfactory bulb interneurons (By similarity). Transcription factor that binds 5'-CNAATTAG-3' DNA sequence. {ECO:0000250|UniProtKB:P31316}.

Recessive Scores

• pRec: 0.137

Haploinsufficiency Scores

• pHI: 0.396
• hipred: Y
• hipred_score: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.421

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gsx2
• Phenotype: growth/size/body region phenotype; taste/olfaction phenotype; craniofacial phenotype; homeostasis/metabolism phenotype; cellular phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); normal 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)

Gene ontology

• Biological process: regulation of respiratory gaseous exchange by neurological system process;regulation of transcription by RNA polymerase II;spinal cord association neuron differentiation;hindbrain morphogenesis;forebrain dorsal/ventral pattern formation;olfactory bulb interneuron differentiation;telencephalon regionalization;regulation of cell migration;positive regulation of Notch signaling pathway;neuron fate specification;positive regulation of oligodendrocyte differentiation;forebrain morphogenesis;subpallium neuron fate commitment
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;sequence-specific DNA binding