GIMAP6

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

Basic information

Region (hg38): 7:150625375-150632648

Links

ENSG00000133561 ∙ NCBI:474344 ∙ OMIM:616960 ∙ HGNC:21918 ∙ Uniprot:Q6P9H5 ∙ 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 GIMAP6 gene.

• not_specified (47 variants)
• not_provided (5 variants)
• Primary_Immune_Deficiency (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GIMAP6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024711.6. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			44	3	3	50
nonsense		1				1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	44	3	4

Highest pathogenic variant AF is 0.000004104669

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GIMAP6	protein_coding	protein_coding	ENST00000328902	2	7011

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.142	0.642	116461	0	1	116462	0.00000429

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.293	151	161	0.935	0.00000967	1870
Missense in 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

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	0.0000472	0.0000472
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

Recessive Scores

• pRec: 0.0791

Intolerance Scores

• loftool: 0.471
• rvis_EVS: 1.06
• rvis_percentile_EVS: 91.58

Haploinsufficiency Scores

• pHI: 0.0548
• hipred: N
• hipred_score: 0.172
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0376

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gimap6
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; immune system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Cellular component: nucleoplasm;cytosol
• Molecular function: GTP binding