GSC2

goosecoid homeobox 2, the group of PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): 22:19146993-19150292

Previous symbols: [ "GSCL" ]

Links

ENSG00000063515 ∙ NCBI:2928 ∙ OMIM:601845 ∙ HGNC:4613 ∙ Uniprot:O15499 ∙ 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 GSC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GSC2 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						0
missense			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	0

Variants in GSC2

This is a list of pathogenic ClinVar variants found in the GSC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-19149074-C-A		not specified	Uncertain significance (Jul 20, 2021)
22-19149076-C-G		not specified	Uncertain significance (Aug 19, 2024)
22-19149076-C-T		not specified	Uncertain significance (Jun 13, 2024)
22-19149079-C-A		not specified	Uncertain significance (Aug 21, 2023)
22-19149084-C-G		not specified	Uncertain significance (Jan 04, 2024)
22-19149095-C-A		not specified	Uncertain significance (Jul 28, 2021)
22-19149674-C-T		not specified	Uncertain significance (Dec 21, 2022)
22-19149695-C-A		not specified	Uncertain significance (Jan 16, 2024)
22-19149720-G-T		not specified	Uncertain significance (Apr 12, 2022)
22-19149729-C-G		not specified	Uncertain significance (Jan 08, 2024)
22-19149748-G-A		not specified	Uncertain significance (Aug 10, 2023)
22-19149764-G-C		not specified	Uncertain significance (Jun 23, 2021)
22-19149793-C-T		not specified	Uncertain significance (Mar 18, 2024)
22-19149799-G-A		not specified	Uncertain significance (Apr 04, 2023)
22-19149817-G-C		not specified	Uncertain significance (Sep 24, 2024)
22-19149868-G-A		not specified	Uncertain significance (Jun 09, 2022)
22-19149895-A-T		not specified	Uncertain significance (Apr 20, 2024)
22-19149913-G-A		not specified	Uncertain significance (Oct 07, 2024)
22-19149913-G-C		not specified	Uncertain significance (Jan 23, 2024)
22-19150031-C-T		not specified	Uncertain significance (Nov 02, 2023)
22-19150052-C-T		not specified	Uncertain significance (Jun 17, 2024)
22-19150069-G-C		not specified	Uncertain significance (Oct 10, 2023)
22-19150099-G-T		not specified	Uncertain significance (Jun 02, 2024)
22-19150104-C-G		not specified	Uncertain significance (Aug 16, 2022)
22-19150115-C-A		not specified	Uncertain significance (Jan 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GSC2	protein_coding	protein_coding	ENST00000086933	3	1708

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00443	0.451	102231	0	1	102232	0.00000489

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.547	69	57.3	1.20	0.00000306	1228
Missense in Polyphen		36	26.12	1.3783		339
Synonymous	0.127	27	27.9	0.969	0.00000157	461
Loss of Function	-0.346	3	2.42	1.24	1.04e-7	61

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)	0.0000113	0.0000113
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have a role in development. May regulate its own transcription. May bind the bicoid consensus sequence TAATCC.

Recessive Scores

• pRec: 0.114

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.220

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gsc2
• Phenotype: normal phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;anatomical structure morphogenesis
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;sequence-specific DNA binding