GAS2L3

growth arrest specific 2 like 3

Basic information

Region (hg38): 12:100573682-100628288

Links

ENSG00000139354 ∙ NCBI:283431 ∙ OMIM:617224 ∙ HGNC:27475 ∙ Uniprot:Q86XJ1 ∙ 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 GAS2L3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GAS2L3 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					2	2
missense			26	4	3	33
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	4	5

Variants in GAS2L3

This is a list of pathogenic ClinVar variants found in the GAS2L3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-100600416-G-A		not specified	Uncertain significance (Mar 23, 2022)
12-100600418-A-G		not specified	Uncertain significance (May 15, 2024)
12-100600423-T-A			Benign (Jul 11, 2018)
12-100600439-G-A		not specified	Uncertain significance (Nov 07, 2023)
12-100600539-C-G		not specified	Uncertain significance (Jan 10, 2023)
12-100601643-A-G		not specified	Likely benign (Aug 16, 2022)
12-100601680-A-G		not specified	Uncertain significance (Nov 03, 2023)
12-100612109-A-G		not specified	Uncertain significance (May 04, 2022)
12-100612118-A-T		not specified	Uncertain significance (Nov 08, 2022)
12-100617800-G-A		not specified	Uncertain significance (Jun 03, 2024)
12-100618453-G-A		not specified	Uncertain significance (Dec 28, 2022)
12-100618534-G-A		not specified	Uncertain significance (Mar 18, 2024)
12-100622288-C-G		not specified	Uncertain significance (Dec 16, 2021)
12-100622299-C-G		not specified	Uncertain significance (Feb 10, 2022)
12-100623617-A-G		not specified	Uncertain significance (Nov 09, 2022)
12-100623647-G-A		not specified	Uncertain significance (May 20, 2024)
12-100623670-G-C		not specified	Uncertain significance (May 29, 2024)
12-100623673-C-G		not specified	Uncertain significance (Jan 10, 2023)
12-100623727-C-T		not specified	Uncertain significance (May 02, 2024)
12-100623847-C-T		not specified	Uncertain significance (Nov 21, 2023)
12-100623848-G-A		not specified	Likely benign (Oct 10, 2023)
12-100623854-C-A		not specified	Uncertain significance (Jan 16, 2024)
12-100623925-C-A		not specified	Uncertain significance (Jan 26, 2023)
12-100623972-A-C		not specified	Uncertain significance (Feb 22, 2023)
12-100623990-G-A			Benign (Nov 17, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GAS2L3	protein_coding	protein_coding	ENST00000539410	8	54604

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.12e-13	0.216	125663	0	83	125746	0.000330

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.131	369	362	1.02	0.0000186	4438
Missense in Polyphen		85	86.696	0.98043		954
Synonymous	-1.23	153	135	1.13	0.00000718	1416
Loss of Function	1.04	23	29.0	0.792	0.00000152	395

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000805	0.000798
Ashkenazi Jewish	0.000618	0.000595
East Asian	0.000272	0.000272
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000390	0.000387
Middle Eastern	0.000272	0.000272
South Asian	0.000163	0.000163
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cytoskeletal linker protein. May promote and stabilize the formation of the actin and microtubule network. {ECO:0000269|PubMed:21561867}.

Recessive Scores

• pRec: 0.0897

Intolerance Scores

• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.27

Haploinsufficiency Scores

• pHI: 0.119
• hipred: N
• hipred_score: 0.321
• ghis: 0.451

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.338

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gas2l3
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; muscle 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: gas2l3
• Affected structure: ventricular system
• Phenotype tag: abnormal
• Phenotype quality: closed

Gene ontology

• Biological process: microtubule cytoskeleton organization;actin cytoskeleton organization
• Cellular component: cytoplasm;microtubule;actin cytoskeleton;microtubule cytoskeleton
• Molecular function: actin binding;protein binding;microtubule binding