GIMAP1

GTPase, IMAP family member 1, the group of GTPases, IMAP

Basic information

Region (hg38): 7:150716605-150724284

Links

ENSG00000213203 ∙ NCBI:170575 ∙ OMIM:608084 ∙ HGNC:23237 ∙ Uniprot:Q8WWP7 ∙ 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 GIMAP1 gene.

• Inborn genetic diseases (7 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GIMAP1 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					1	1
missense			7		1	8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	2

Variants in GIMAP1

This is a list of pathogenic ClinVar variants found in the GIMAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-150720100-T-A			Benign (Jan 08, 2018)
7-150720269-T-C			Benign (Jan 08, 2018)
7-150720477-C-T		not specified	Uncertain significance (Feb 23, 2023)
7-150720518-C-T		not specified	Uncertain significance (Feb 13, 2024)
7-150720528-G-A		not specified	Uncertain significance (Mar 06, 2023)
7-150720540-C-A		not specified	Uncertain significance (Sep 14, 2023)
7-150720575-C-T		not specified	Uncertain significance (Sep 15, 2021)
7-150720599-G-A		not specified	Uncertain significance (Aug 02, 2022)
7-150720729-G-A		not specified	Uncertain significance (Dec 21, 2023)
7-150720818-A-G		not specified	Uncertain significance (May 05, 2023)
7-150720822-G-A		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GIMAP1	protein_coding	protein_coding	ENST00000307194	2	7728

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.404	0.479	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.874	169	204	0.828	0.0000144	1927
Missense in Polyphen		47	64.304	0.7309		682
Synonymous	0.421	88	93.2	0.945	0.00000672	654
Loss of Function	0.968	0	1.09	0.00	4.64e-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: May regulate lymphocyte survival. Required for normal levels of mature T-lymphocytes and mature B-cells (By similarity). {ECO:0000250}.

Intolerance Scores

• loftool: 0.0784
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.27

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.455
• ghis: 0.512

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.256

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gimap1
• Phenotype: immune system phenotype; hematopoietic system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Cellular component: Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: GTP binding