GIMAP5

GTPase, IMAP family member 5, the group of GTPases, IMAP

Basic information

Region (hg38): 7:150722253-150750033

Previous symbols: [ "IAN4L1" ]

Links

ENSG00000196329 ∙ NCBI:55340 ∙ OMIM:608086 ∙ HGNC:18005 ∙ Uniprot:Q96F15 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• portal hypertension, noncirrhotic, 2 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Portal hypertension, noncirrhotic, 2	AR	Allergy/Immunology/Infectious; Gastrointestinal; Hematologic	The condition has been described as involving susceptibility to infections and autoimmune hemolytic disease, and awareness may allow early diagnosis and management; Individuals have been described as suffering from liver failures, and awareness may allow medidcal management of sequelae	Allergy/Immunology/Infectious; Gastrointestinal; Hematologic	33956074

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GIMAP5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GIMAP5 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	2
missense			2	1		3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5	1		6
Total	0	0	7	3	1

Variants in GIMAP5

This is a list of pathogenic ClinVar variants found in the GIMAP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-150737538-C-T		not specified	Uncertain significance (Aug 21, 2023)
7-150737553-G-A		not specified	Likely benign (Jun 17, 2022)
7-150737572-G-C		not specified	Uncertain significance (Mar 12, 2024)
7-150737605-G-A		not specified	Uncertain significance (Feb 28, 2023)
7-150737646-G-A		not specified	Uncertain significance (Aug 30, 2022)
7-150737687-C-G		not specified	Uncertain significance (Sep 14, 2022)
7-150742279-T-C		Portal hypertension • Portal hypertension, noncirrhotic, 2	Pathogenic/Likely pathogenic (Aug 03, 2021)
7-150742422-G-C		not specified	Uncertain significance (Dec 11, 2023)
7-150742465-C-T		Portal hypertension • Portal hypertension, noncirrhotic, 2	Pathogenic/Likely pathogenic (Aug 02, 2021)
7-150742584-C-G		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
7-150742671-C-T		not specified	Uncertain significance (Apr 14, 2022)
7-150742672-G-A		not specified	Likely benign (Aug 28, 2023)
7-150742750-T-C		Portal hypertension, noncirrhotic, 2 • Portal hypertension	Conflicting classifications of pathogenicity (Jan 04, 2024)
7-150742806-C-T		Portal hypertension • Portal hypertension, noncirrhotic, 2	Pathogenic/Likely pathogenic (Aug 03, 2021)
7-150742880-C-A			Likely benign (Jun 01, 2022)
7-150742952-G-A			Benign (Dec 11, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GIMAP5	protein_coding	protein_coding	ENST00000358647	2	27781

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0965	0.593	125694	0	3	125697	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.551	183	163	1.12	0.00000860	1988
Missense in Polyphen		62	58.523	1.0594		735
Synonymous	-1.19	83	70.3	1.18	0.00000397	591
Loss of Function	0.0931	1	1.11	0.904	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	0.0000924	0.0000924
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for mitochondrial integrity and T-cell survival. May contribute to T-cell quiescence (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.540
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.73

Haploinsufficiency Scores

• pHI: 0.0849
• hipred: N
• hipred_score: 0.145
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00141

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gimap5
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; liver/biliary system phenotype; hematopoietic system 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); digestive/alimentary phenotype; immune system phenotype

Gene ontology

• Cellular component: mitochondrial outer membrane;lysosome;endoplasmic reticulum;integral component of membrane
• Molecular function: protein binding;GTP binding