GIMAP6

protein-coding

GTPase, IMAP family member 6, the group of GTPases, IMAP

Gene summary

This gene encodes a member of the GTPases of immunity-associated proteins (GIMAP) family. GIMAP proteins contain GTP-binding and coiled-coil motifs, and may play roles in the regulation of cell survival. Decreased expression of this gene may play a role in non-small cell lung cancer. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, which is found in a cluster with seven additional GIMAP genes on the long arm of chromosome 7. [provided by RefSeq, Sep 2011]

MANE transcript

NM_024711.6

Inheritance

ClinVar variants

P:1U:51B:9

Top phenotype

autoinflammatory syndrome

gnomAD constraint

pLI —, LoF o/e 0.52

Max pathogenic AF

—

Genomic locus

chr7:150,625,375-150,632,648

External References & Databases

Ensembl (ENSG00000133561)

Transcript & Mutation Effects

hg38 • Region Span ~7.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

autoinflammatory syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0019751

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GIMAP6 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 54

not providedTotal: 5

Primary ciliary dyskinesiaTotal: 2

Primary Immune DeficiencyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024711.6. 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			49 clinvar	5 clinvar	3 clinvar	57
nonsense		1 clinvar				1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	1	51	5	4	61

Highest pathogenic variant AF is 0.000004104669

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024711.6	RefSeq	NP_078987.3	2	MANE Select
ENST00000328902.9	Ensembl	ENSP00000330374.5	2	MANE Select
NM_001244071.2	RefSeq	NP_001231000.1	2	Standard
NM_001244072.2	RefSeq	NP_001231001.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

GTP binding

Cellular Component

nucleoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000328902
Coding exons: 2
Length: 7011
Individuals with no LoFs: 116461
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 116462
p: 0.00000429

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.293	151	161	0.935	0.00000967	1870
Missense (PolyPhen)		49	55.518	0.8826		647
Synonymous	-1.29	86	72.1	1.19	0.00000453	602
Loss of Function	0.620	1	1.93	0.518	8.18e-8	22

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	0.000047	0.000047	rare
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0791

Intolerance Scores

LoFtool: 0.471
RVIS EVS: 1.06
RVIS percentile EVS: 91.58

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0376

Gene Damage Prediction

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