GIMAP2

protein-coding

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

Gene summary

This gene encodes a protein belonging to the GTP-binding superfamily and to the immuno-associated nucleotide (IAN) subfamily of nucleotide-binding proteins. In humans, the IAN subfamily genes are located in a cluster at 7q36.1. [provided by RefSeq, Jul 2008]

MANE transcript

NM_015660.3

Inheritance

—

ClinVar variants

U:48B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr7:150,685,697-150,693,641

External References & Databases

Ensembl (ENSG00000106560)

Transcript & Mutation Effects

hg38 • Region Span ~7.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GIMAP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 49

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015660.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			47 clinvar	6 clinvar		53
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	48	6	0	54

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015660.3	RefSeq	NP_056475.1	2	MANE Select
ENST00000223293.10	Ensembl	ENSP00000223293.5	2	MANE Select
ENST00000474605.1	Ensembl	ENSP00000420423.1	2	Standard
ENST00000474605.2	Ensembl	ENSP00000420423.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

TYROBP Causal Network

Molecular Function

protein binding
GTP binding
identical protein binding

Cellular Component

endoplasmic reticulum
lipid droplet
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000223293
Coding exons: 2
Length: 7945
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.118	170	174	0.975	0.00000820	2234
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0670

Intolerance Scores

LoFtool: 0.839
RVIS EVS: 0.97
RVIS percentile EVS: 90.34

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.142

Gene Damage Prediction

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