GSG1L

GSG1 like

Basic information

Region (hg38): 16:27787527-28063714

Links

ENSG00000169181 ∙ NCBI:146395 ∙ OMIM:617161 ∙ HGNC:28283 ∙ Uniprot:Q6UXU4 ∙ 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 GSG1L gene.

• Inborn genetic diseases (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GSG1L 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in GSG1L

This is a list of pathogenic ClinVar variants found in the GSG1L region.

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

Position	Type	Phenotype	Significance	ClinVar
16-27791401-C-T		not specified	Uncertain significance (Mar 06, 2023)
16-27807502-C-T		not specified	Uncertain significance (Aug 22, 2023)
16-27807516-A-G		not specified	Uncertain significance (May 26, 2023)
16-27807538-C-T		not specified	Uncertain significance (May 17, 2023)
16-27828796-G-A		not specified	Uncertain significance (Oct 29, 2021)
16-27828798-A-G		not specified	Uncertain significance (Feb 07, 2023)
16-27828888-G-A		not specified	Uncertain significance (Feb 14, 2023)
16-27828909-G-A		not specified	Uncertain significance (Oct 31, 2023)
16-27845005-T-C		not specified	Uncertain significance (Feb 23, 2023)
16-27884519-T-C		not specified	Uncertain significance (Aug 02, 2022)
16-27884552-G-A		not specified	Uncertain significance (Mar 11, 2024)
16-27884561-C-T		not specified	Uncertain significance (Feb 28, 2023)
16-28063180-G-C		not specified	Uncertain significance (Oct 26, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GSG1L	protein_coding	protein_coding	ENST00000447459	7	275981

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.768	0.232	125729	0	7	125736	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	114	150	0.759	0.00000927	2104
Missense in Polyphen		49	69.471	0.70533		954
Synonymous	0.334	61	64.4	0.947	0.00000448	649
Loss of Function	2.91	2	13.6	0.147	7.60e-7	161

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000581	0.0000581
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As a component of the inner core of AMPAR complex, modifies AMPA receptor (AMPAR) gating. {ECO:0000250}.

Haploinsufficiency Scores

• pHI: 0.148
• hipred: Y
• hipred_score: 0.699
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.116

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gsg1l

Gene ontology

• Biological process: regulation of postsynaptic neurotransmitter receptor internalization;regulation of AMPA receptor activity
• Cellular component: plasma membrane;cell junction;Schaffer collateral - CA1 synapse;glutamatergic synapse;integral component of postsynaptic density membrane
• Molecular function: protein binding