GIMAP4

GTPase, IMAP family member 4, the group of GTPases, IMAP

Basic information

Region (hg38): 7:150567368-150573953

Links

ENSG00000133574 ∙ NCBI:55303 ∙ OMIM:608087 ∙ HGNC:21872 ∙ Uniprot:Q9NUV9 ∙ 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 GIMAP4 gene.

• Inborn genetic diseases (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GIMAP4 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						0
missense			13	2		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	2	0

Variants in GIMAP4

This is a list of pathogenic ClinVar variants found in the GIMAP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-150569921-G-A		not specified	Uncertain significance (Feb 11, 2022)
7-150569934-C-A		not specified	Uncertain significance (Nov 08, 2022)
7-150569935-C-G		not specified	Uncertain significance (Aug 20, 2023)
7-150569935-C-T		not specified	Uncertain significance (Mar 07, 2024)
7-150572168-T-C		not specified	Uncertain significance (Oct 29, 2021)
7-150572174-T-C		not specified	Uncertain significance (Jan 24, 2024)
7-150572227-C-T		not specified	Uncertain significance (Feb 10, 2022)
7-150572228-G-A		not specified	Likely benign (Jun 22, 2023)
7-150572257-A-C		not specified	Uncertain significance (Dec 15, 2023)
7-150572263-A-G		not specified	Uncertain significance (Sep 26, 2023)
7-150572287-A-G		not specified	Uncertain significance (Oct 26, 2021)
7-150572288-G-T		not specified	Uncertain significance (Jun 28, 2022)
7-150572333-G-A		not specified	Uncertain significance (Dec 21, 2023)
7-150572422-C-T		not specified	Uncertain significance (Oct 27, 2021)
7-150572485-A-C		not specified	Uncertain significance (Jan 10, 2023)
7-150572521-C-T		not specified	Uncertain significance (Dec 07, 2021)
7-150572702-G-A		not specified	Uncertain significance (Jan 09, 2024)
7-150572753-G-A		not specified	Likely benign (Jun 24, 2022)
7-150572830-C-T		not specified	Uncertain significance (Feb 28, 2024)
7-150572833-A-G		not specified	Uncertain significance (Jan 27, 2022)
7-150572911-A-G		not specified	Uncertain significance (Jan 04, 2022)
7-150572936-A-G		not specified	Uncertain significance (Mar 25, 2022)
7-150572953-C-G		not specified	Uncertain significance (Oct 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GIMAP4	protein_coding	protein_coding	ENST00000255945	2	6677

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00174	0.290	125640	0	3	125643	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.271	202	191	1.06	0.0000110	2165
Missense in Polyphen		51	53.696	0.94979		730
Synonymous	0.624	65	71.7	0.906	0.00000432	627
Loss of Function	-1.67	3	1.11	2.71	4.70e-8	12

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in regulating lymphocyte apoptosis (By similarity). Exhibits intrisinic GTPase activity. Shows a higher affinity for GDP over GTP (about 12-fold higher), and binding shows an absolute requirement for magnesium. {ECO:0000250}.

Recessive Scores

• pRec: 0.0646

Intolerance Scores

• loftool: 0.682
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.38

Haploinsufficiency Scores

• pHI: 0.0346
• hipred: N
• hipred_score: 0.112
• ghis: 0.440

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.144

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gimap4
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Cellular component: cytosol
• Molecular function: GTP binding