GIMAP4

protein-coding

GTPase, IMAP family member 4, 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. The encoded protein of this gene may be negatively regulated by T-cell acute lymphocytic leukemia 1 (TAL1). In humans, the IAN subfamily genes are located in a cluster at 7q36.1. [provided by RefSeq, Jul 2008]

MANE transcript

NM_018326.3

Inheritance

—

ClinVar variants

U:53B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 2.71

Max pathogenic AF

—

Genomic locus

chr7:150,567,369-150,573,953

External References & Databases

Ensembl (ENSG00000133574)

Transcript & Mutation Effects

hg38 • Region Span ~6.6 kb

Loading mutation effect viewer...

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 GIMAP4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 58

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018326.3. 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						0
missense			53 clinvar	5 clinvar		58
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	53	5	0	58

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018326.3	RefSeq	NP_060796.1	2	MANE Select
ENST00000255945.4	Ensembl	ENSP00000255945.2	2	MANE Select
NM_001363532.2	RefSeq	NP_001350461.1	2	Standard
ENST00000461940.5	Ensembl	ENSP00000419545.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

GTP binding

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000255945
Coding exons: 2
Length: 6677
Individuals with no LoFs: 125640
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125643
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.271	202	191	1.06	0.0000110	2165
Missense (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

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)	0.000027	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.144

Gene Damage Prediction

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