GIMAP2

GTPase, IMAP family member 2, the group of GTPases, IMAP

Basic information

Region (hg38): 7:150685696-150693641

Links

ENSG00000106560 ∙ NCBI:26157 ∙ OMIM:608085 ∙ HGNC:21789 ∙ Uniprot:Q9UG22 ∙ 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 GIMAP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GIMAP2 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			23	2		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	0

Variants in GIMAP2

This is a list of pathogenic ClinVar variants found in the GIMAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-150692365-C-G		not specified	Uncertain significance (Feb 26, 2024)
7-150692408-G-A		not specified	Uncertain significance (Aug 13, 2021)
7-150692433-A-C		not specified	Uncertain significance (Jan 26, 2023)
7-150692486-G-T			Likely benign (Nov 01, 2022)
7-150692544-C-A		not specified	Uncertain significance (Apr 12, 2022)
7-150692548-T-A		not specified	Likely benign (Jul 06, 2022)
7-150692576-G-A		not specified	Uncertain significance (Nov 09, 2022)
7-150692603-C-T		not specified	Uncertain significance (Aug 30, 2021)
7-150692660-C-G		not specified	Uncertain significance (Sep 14, 2022)
7-150692675-A-C		not specified	Uncertain significance (Apr 14, 2022)
7-150692737-C-T		not specified	Uncertain significance (Jan 20, 2023)
7-150692764-A-T		not specified	Uncertain significance (Mar 05, 2024)
7-150692770-G-A		not specified	Likely benign (Apr 12, 2024)
7-150692785-G-A		not specified	Uncertain significance (Feb 16, 2023)
7-150692795-A-G		not specified	Uncertain significance (Oct 25, 2023)
7-150692819-G-A		not specified	Uncertain significance (Sep 17, 2021)
7-150692855-A-G		not specified	Uncertain significance (Apr 24, 2023)
7-150692860-G-A		not specified	Uncertain significance (Oct 18, 2021)
7-150693018-A-G		not specified	Uncertain significance (Sep 13, 2022)
7-150693037-A-G		not specified	Uncertain significance (Oct 21, 2021)
7-150693041-G-C		not specified	Uncertain significance (Dec 14, 2023)
7-150693041-G-T		not specified	Uncertain significance (Oct 25, 2022)
7-150693044-A-G		not specified	Uncertain significance (Dec 19, 2022)
7-150693268-A-T		not specified	Uncertain significance (Oct 04, 2022)
7-150693280-C-T		not specified	Uncertain significance (Sep 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GIMAP2	protein_coding	protein_coding	ENST00000223293	2	7945

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.405	0.479	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.118	170	174	0.975	0.00000820	2234
Missense in Polyphen		48	45.84	1.0471		596
Synonymous	0.486	60	65.0	0.923	0.00000298	626
Loss of Function	0.974	0	1.11	0.00	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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The heterodimer formed by GIMAP2 and GIMAP7 has GTPase activity. In contrast, GIMAP2 has no GTPase activity by itself. {ECO:0000269|PubMed:23454188}.
• Pathway: TYROBP Causal Network (Consensus)

Recessive Scores

• pRec: 0.0670

Intolerance Scores

• loftool: 0.839
• rvis_EVS: 0.97
• rvis_percentile_EVS: 90.34

Haploinsufficiency Scores

• pHI: 0.0576
• hipred: N
• hipred_score: 0.123
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.142

Gene Damage Prediction

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

Gene ontology

• Cellular component: endoplasmic reticulum;lipid droplet;integral component of membrane
• Molecular function: protein binding;GTP binding;identical protein binding