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.

not_specified (30 variants)
Hearing_loss,_autosomal_recessive_125 (2 variants)
not_provided (1 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. These statistics are base on transcript: NM_001143830.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense		1 clinvar	30 clinvar			31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)	1 clinvar					1
Total	1	1	30	0	1

Highest pathogenic variant AF is 6.93643e-7

Loading clinvar variants...

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