GAS2L1

growth arrest specific 2 like 1

Basic information

Region (hg38): 22:29306618-29312787

Links

ENSG00000185340 ∙ NCBI:10634 ∙ OMIM:602128 ∙ HGNC:16955 ∙ Uniprot:Q99501 ∙ 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 GAS2L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GAS2L1 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			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	0

Variants in GAS2L1

This is a list of pathogenic ClinVar variants found in the GAS2L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-29308124-G-A		not specified	Uncertain significance (Aug 05, 2024)
22-29308146-A-G		not specified	Uncertain significance (Oct 26, 2022)
22-29308163-C-A		not specified	Uncertain significance (Jan 03, 2024)
22-29308164-G-A		not specified	Uncertain significance (Jan 20, 2025)
22-29308232-C-G		not specified	Uncertain significance (Aug 14, 2023)
22-29308269-G-C		not specified	Uncertain significance (Jul 20, 2021)
22-29308284-C-T		not specified	Uncertain significance (Jun 30, 2024)
22-29308310-G-A		not specified	Uncertain significance (Mar 10, 2025)
22-29308361-G-A		not specified	Uncertain significance (Aug 08, 2022)
22-29308371-C-G		not specified	Uncertain significance (Jul 26, 2024)
22-29308454-C-G		not specified	Uncertain significance (Oct 26, 2021)
22-29308510-C-A		not specified	Uncertain significance (Aug 14, 2024)
22-29308550-C-T		not specified	Uncertain significance (Nov 13, 2024)
22-29308581-A-C		not specified	Uncertain significance (Oct 26, 2022)
22-29308616-G-A		not specified	Uncertain significance (Oct 25, 2022)
22-29308628-C-G		not specified	Uncertain significance (Feb 23, 2023)
22-29308658-A-G		not specified	Uncertain significance (Apr 12, 2024)
22-29308673-G-T		not specified	Uncertain significance (Nov 15, 2024)
22-29308691-C-T		not specified	Uncertain significance (Jan 23, 2025)
22-29308698-C-T		not specified	Uncertain significance (Feb 18, 2025)
22-29308701-G-T		not specified	Uncertain significance (Sep 22, 2023)
22-29310524-C-T		not specified	Uncertain significance (May 12, 2024)
22-29310845-C-T		not specified	Uncertain significance (Aug 13, 2021)
22-29310890-G-T		not specified	Uncertain significance (Feb 06, 2025)
22-29310904-A-G		not specified	Uncertain significance (Sep 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GAS2L1	protein_coding	protein_coding	ENST00000341313	4	6203

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.832	0.167	125725	0	4	125729	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.33	169	225	0.750	0.0000158	2086
Missense in Polyphen		91	141.34	0.64384		1348
Synonymous	1.22	83	98.4	0.843	0.00000711	742
Loss of Function	2.68	1	10.3	0.0975	6.03e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000287	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Seems to be involved in the cross-linking of microtubules and microfilaments. {ECO:0000269|PubMed:12584248}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in squamous cell - TarBase;Ectoderm Differentiation (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.520
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.29

Haploinsufficiency Scores

• pHI: 0.317
• hipred: Y
• hipred_score: 0.617
• ghis: 0.449

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0396

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gas2l1
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: cell cycle arrest;cellular response to starvation;cellular response to thyroid hormone stimulus
• Cellular component: cytoplasm;cytoskeleton
• Molecular function: microtubule binding;cytoskeletal adaptor activity;thyroid hormone receptor binding