GAS2

growth arrest specific 2

Basic information

Region (hg38): 11:22625509-22813001

Links

ENSG00000148935 ∙ NCBI:2620 ∙ OMIM:602835 ∙ HGNC:4167 ∙ Uniprot:O43903 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hearing loss, autosomal recessive 125 (Limited), mode of inheritance: AR
• hearing loss disorder (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal recessive, 25	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic	33964205

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GAS2 gene.

• Fanconi anemia (9 variants)
• Fanconi anemia complementation group F (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GAS2 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	1
missense			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	9	11	75	36	3	134
Total	9	11	91	36	4

Highest pathogenic variant AF is 0.0000197

Variants in GAS2

This is a list of pathogenic ClinVar variants found in the GAS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-22625510-G-A		not specified	Uncertain significance (Sep 01, 2021)
11-22625510-G-C		Fanconi anemia • Fanconi anemia complementation group F	Uncertain significance (Feb 20, 2024)
11-22625511-G-C		Fanconi anemia complementation group F	Uncertain significance (Apr 07, 2024)
11-22625519-G-A		Fanconi anemia	Likely benign (Apr 28, 2023)
11-22625520-C-G		Fanconi anemia	Likely benign (Nov 23, 2021)
11-22625520-C-T		Fanconi anemia	Likely benign (Sep 09, 2022)
11-22625521-A-G		Inborn genetic diseases	Uncertain significance (Jan 16, 2025)
11-22625526-CAG-C		Fanconi anemia complementation group F	Pathogenic (Jun 06, 2022)
11-22625530-G-A		Fanconi anemia	Uncertain significance (Jan 24, 2022)
11-22625530-G-C		Fanconi anemia	Uncertain significance (Sep 05, 2023)
11-22625532-G-A		Fanconi anemia • Fanconi anemia complementation group F • not specified	Conflicting classifications of pathogenicity (Oct 05, 2024)
11-22625533-A-G		Fanconi anemia complementation group F	Uncertain significance (Feb 27, 2024)
11-22625534-G-A		Fanconi anemia	Uncertain significance (Feb 24, 2024)
11-22625535-C-G		Fanconi anemia	Likely benign (Oct 13, 2023)
11-22625541-G-A		Fanconi anemia	Uncertain significance (Jun 13, 2024)
11-22625542-T-C		Fanconi anemia	Uncertain significance (Nov 28, 2023)
11-22625542-TCA-T		Fanconi anemia • Fanconi anemia complementation group F	Pathogenic/Likely pathogenic (Aug 10, 2023)
11-22625543-C-T		Fanconi anemia	Uncertain significance (Sep 29, 2021)
11-22625544-A-G		Fanconi anemia	Likely benign (Feb 23, 2024)
11-22625547-GTGA-G		Fanconi anemia	Uncertain significance (Jun 14, 2016)
11-22625551-C-A		Fanconi anemia	Uncertain significance (Jul 19, 2022)
11-22625553-G-A		Fanconi anemia	Likely benign (Nov 27, 2024)
11-22625553-G-T		Fanconi anemia	Likely benign (Jan 22, 2025)
11-22625555-G-A		not specified	not provided (Sep 19, 2013)
11-22625558-C-T		Fanconi anemia	Uncertain significance (May 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GAS2	protein_coding	protein_coding	ENST00000454584	7	187414

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000802	0.985	125730	0	17	125747	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.440	154	170	0.905	0.00000876	2039
Missense in Polyphen		39	56.149	0.69457		641
Synonymous	0.161	60	61.6	0.974	0.00000312	599
Loss of Function	2.15	8	17.8	0.449	0.00000110	201

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000176	0.000176
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000706	0.0000703
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000655	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in apoptosis by acting as a cell death substrate for caspases. Is cleaved during apoptosis and the cleaved form induces dramatic rearrangements of the actin cytoskeleton and potent changes in the shape of the affected cells. May be involved in the membrane ruffling process (By similarity). {ECO:0000250}.
• Pathway: induction of apoptosis through dr3 and dr4/5 death receptors;Caspase-mediated cleavage of cytoskeletal proteins;Apoptotic cleavage of cellular proteins;Apoptotic execution phase;Apoptosis;Programmed Cell Death;Caspase Cascade in Apoptosis (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.724
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.82

Haploinsufficiency Scores

• pHI: 0.536
• hipred: Y
• hipred_score: 0.617
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.845

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gas2
• Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: initiation of primordial ovarian follicle growth;antral ovarian follicle growth;apoptotic process;cell cycle arrest;regulation of cell shape;regulation of Notch signaling pathway;ovulation;basement membrane organization
• Cellular component: cytosol;actin filament;membrane
• Molecular function: microtubule binding