GIT2

GIT ArfGAP 2, the group of ArfGAPs|Ankyrin repeat domain containing

Basic information

Region (hg38): 12:109929803-109996389

Links

ENSG00000139436 ∙ NCBI:9815 ∙ OMIM:608564 ∙ HGNC:4273 ∙ Uniprot:Q14161 ∙ 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 GIT2 gene.

• Inborn genetic diseases (18 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GIT2 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					3	3
missense			18	1	2	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	5

Variants in GIT2

This is a list of pathogenic ClinVar variants found in the GIT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-109933156-C-T		not specified	Uncertain significance (Dec 01, 2022)
12-109934057-C-T		not specified	Uncertain significance (Oct 18, 2021)
12-109938533-C-G		not specified	Uncertain significance (Oct 30, 2023)
12-109939178-G-A		not specified	Uncertain significance (Dec 20, 2023)
12-109945268-C-T		not specified	Likely benign (Jan 23, 2024)
12-109945333-A-C		not specified	Uncertain significance (Dec 14, 2022)
12-109945336-G-A			Benign (Jul 13, 2018)
12-109945340-T-G		not specified	Uncertain significance (Aug 12, 2022)
12-109947264-G-A		not specified	Uncertain significance (Feb 26, 2024)
12-109947294-C-T		not specified	Uncertain significance (Apr 10, 2023)
12-109947375-G-A		not specified	Uncertain significance (Jan 04, 2022)
12-109951190-C-T		not specified	Uncertain significance (Oct 20, 2021)
12-109951246-A-T		not specified	Uncertain significance (Jan 19, 2024)
12-109951247-C-A		not specified	Uncertain significance (Aug 23, 2021)
12-109953098-C-T			Benign (Apr 05, 2018)
12-109953168-T-C		not specified	Uncertain significance (Jan 23, 2023)
12-109953174-T-C			Benign (Aug 22, 2019)
12-109959858-G-A		not specified	Uncertain significance (Dec 21, 2023)
12-109959894-C-T		not specified	Uncertain significance (Jan 19, 2024)
12-109959915-G-A		not specified	Uncertain significance (Oct 26, 2021)
12-109959933-T-C			Likely benign (Aug 20, 2018)
12-109961330-G-A		not specified	Uncertain significance (Feb 17, 2022)
12-109961353-G-T		not specified	Uncertain significance (Aug 22, 2023)
12-109961649-C-T		not specified	Uncertain significance (Oct 05, 2021)
12-109965530-T-C		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GIT2	protein_coding	protein_coding	ENST00000355312	20	66588

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00207	125736	0	10	125746	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.34	315	456	0.691	0.0000264	4995
Missense in Polyphen		101	178.53	0.56572		1959
Synonymous	0.806	167	181	0.924	0.0000123	1447
Loss of Function	5.35	6	44.5	0.135	0.00000229	502

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000332	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase-activating protein for the ADP ribosylation factor family.
• Pathway: Endocytosis - Homo sapiens (human);Integrin-mediated Cell Adhesion;TCR;EGFR1;agrin in postsynaptic differentiation;Integrin-linked kinase signaling;Signaling events mediated by focal adhesion kinase (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.444
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.73

Haploinsufficiency Scores

• pHI: 0.158
• hipred: Y
• hipred_score: 0.694
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.971

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Git2
• Phenotype: immune system phenotype; hematopoietic system phenotype; normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: git2a
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: kinked

Gene ontology

• Biological process: regulation of G protein-coupled receptor signaling pathway;positive regulation of GTPase activity
• Cellular component: nucleoplasm;focal adhesion
• Molecular function: GTPase activator activity;protein binding;metal ion binding