GIT1

GIT ArfGAP 1, the group of Ankyrin repeat domain containing|ArfGAPs

Basic information

Region (hg38): 17:29573475-29594054

Links

ENSG00000108262 ∙ NCBI:28964 ∙ OMIM:608434 ∙ HGNC:4272 ∙ Uniprot:Q9Y2X7 ∙ 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 GIT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GIT1 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				11	2	13
missense			28	1		29
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				1	1	2
Total	0	0	29	13	3

Variants in GIT1

This is a list of pathogenic ClinVar variants found in the GIT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-29574693-GGA-G		GIT1-related disorder	Likely benign (May 07, 2019)
17-29574837-C-T		GIT1-related disorder	Likely benign (Jul 12, 2019)
17-29574859-T-C		Inborn genetic diseases	Uncertain significance (Jan 29, 2024)
17-29574869-C-T		Inborn genetic diseases	Uncertain significance (Jan 26, 2023)
17-29575146-C-T		GIT1-related disorder	Likely benign (Jun 07, 2019)
17-29575431-T-C		GIT1-related disorder	Likely benign (May 21, 2020)
17-29575453-A-T		Inborn genetic diseases	Uncertain significance (Oct 19, 2023)
17-29575463-C-A		Inborn genetic diseases	Uncertain significance (Jun 26, 2023)
17-29575666-T-G		Inborn genetic diseases	Uncertain significance (Jun 29, 2023)
17-29575675-G-C		Inborn genetic diseases	Uncertain significance (Mar 20, 2024)
17-29575813-G-A		Inborn genetic diseases	Uncertain significance (Jun 05, 2023)
17-29575856-A-C		Inborn genetic diseases	Uncertain significance (Mar 04, 2024)
17-29576079-C-T		Inborn genetic diseases	Uncertain significance (Mar 20, 2024)
17-29576080-G-A		Inborn genetic diseases	Uncertain significance (Dec 01, 2022)
17-29576092-C-T		Inborn genetic diseases	Uncertain significance (May 28, 2024)
17-29576102-C-T		GIT1-related disorder	Likely benign (Jan 03, 2020)
17-29576104-C-A		Inborn genetic diseases	Uncertain significance (Sep 26, 2023)
17-29576239-A-G		Inborn genetic diseases	Uncertain significance (Sep 25, 2023)
17-29576262-A-AG		Developmental disorder	Uncertain significance (Jul 13, 2021)
17-29576275-A-T		Inborn genetic diseases	Uncertain significance (Dec 18, 2023)
17-29576283-C-G		GIT1-related disorder	Likely benign (May 23, 2019)
17-29576286-G-A		GIT1-related disorder	Likely benign (Jun 12, 2019)
17-29576368-G-A		Inborn genetic diseases	Uncertain significance (Jan 26, 2023)
17-29576369-C-T		Inborn genetic diseases	Uncertain significance (Dec 02, 2022)
17-29576372-G-A		Inborn genetic diseases	Uncertain significance (Mar 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GIT1	protein_coding	protein_coding	ENST00000394869	21	20586

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000223	125734	0	5	125739	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.06	294	483	0.608	0.0000316	4974
Missense in Polyphen		81	179.83	0.45042		1848
Synonymous	0.658	193	205	0.942	0.0000141	1555
Loss of Function	5.41	4	41.7	0.0960	0.00000210	463

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000944	0.0000924
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000349	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase-activating protein for the ADP ribosylation factor family. May serve as a scaffold to bring together molecules to form signaling modules controlling vesicle trafficking, adhesion and cytoskeletal organization. Increases the speed of cell migration, as well as the size and rate of formation of protrusions, possibly by targeting PAK1 to adhesions and the leading edge of lamellipodia. Sequesters inactive non-tyrosine- phosphorylated paxillin in cytoplasmic complexes. Involved in the regulation of cytokinesis; the function may involve ENTR1 and PTPN13 (By similarity). {ECO:0000250|UniProtKB:Q68FF6, ECO:0000269|PubMed:11896197}.
• Pathway: Endocytosis - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human);Regulation of Actin Cytoskeleton;Developmental Biology;EPH-Ephrin signaling;Ephrin signaling;Aurora A signaling;EGFR1;Axon guidance;Stabilization and expansion of the E-cadherin adherens junction;Regulation of CDC42 activity;Arf6 signaling events;Alpha4 beta1 integrin signaling events (Consensus)

Recessive Scores

• pRec: 0.176

Intolerance Scores

• loftool: 0.355
• rvis_EVS: -1.4
• rvis_percentile_EVS: 4.19

Haploinsufficiency Scores

• pHI: 0.451
• hipred: Y
• hipred_score: 0.825
• ghis: 0.661

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.843

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Git1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); normal 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)

Zebrafish Information Network

• Gene name: git1
• Affected structure: central artery
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: regulation of G protein-coupled receptor signaling pathway;regulation of cytokinesis;positive regulation of GTPase activity;ephrin receptor signaling pathway;presynaptic modulation of chemical synaptic transmission;regulation of synaptic vesicle exocytosis
• Cellular component: cytosol;focal adhesion;membrane;calyx of Held
• Molecular function: GTPase activator activity;protein binding;protein-containing complex binding;metal ion binding