GAREM1

GRB2 associated regulator of MAPK1 subtype 1

Basic information

Region (hg38): 18:32124876-32470882

Previous symbols: [ "C18orf11", "FAM59A", "GAREM" ]

Links

ENSG00000141441 ∙ NCBI:64762 ∙ OMIM:617998 ∙ HGNC:26136 ∙ Uniprot:Q9H706 ∙ 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 GAREM1 gene.

• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GAREM1 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						0
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in GAREM1

This is a list of pathogenic ClinVar variants found in the GAREM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-32190123-T-C		not specified	Uncertain significance (Sep 27, 2021)
18-32192685-A-G		not specified	Uncertain significance (Dec 02, 2022)
18-32195471-T-C		not specified	Uncertain significance (Jul 14, 2023)
18-32195471-T-G		not specified	Uncertain significance (Dec 06, 2022)
18-32202916-C-T		not specified	Uncertain significance (Dec 14, 2023)
18-32202963-G-T		not specified	Uncertain significance (Mar 06, 2023)
18-32204205-G-A		not specified	Uncertain significance (Jun 24, 2022)
18-32204234-G-T		not specified	Uncertain significance (Sep 13, 2022)
18-32204253-T-C		not specified	Uncertain significance (Oct 02, 2023)
18-32204258-A-T		not specified	Uncertain significance (Feb 13, 2024)
18-32204306-T-A		not specified	Uncertain significance (Dec 06, 2022)
18-32204307-C-T		not specified	Uncertain significance (Feb 09, 2022)
18-32207437-G-C		not specified	Uncertain significance (Dec 21, 2023)
18-32208211-C-T		not specified	Uncertain significance (Jul 15, 2021)
18-32208239-A-G		not specified	Uncertain significance (Dec 15, 2022)
18-32208254-A-G		not specified	Uncertain significance (Nov 27, 2023)
18-32210545-G-C		not specified	Uncertain significance (Aug 10, 2021)
18-32210549-C-A		not specified	Uncertain significance (Dec 15, 2023)
18-32213193-C-T		not specified	Uncertain significance (Jul 06, 2021)
18-32213233-A-G		not specified	Uncertain significance (Oct 06, 2022)
18-32213260-G-T		not specified	Uncertain significance (Mar 01, 2023)
18-32213269-A-T		not specified	Uncertain significance (Sep 29, 2023)
18-32213502-A-G		not specified	Uncertain significance (Jul 06, 2021)
18-32213511-C-T		not specified	Uncertain significance (Dec 15, 2023)
18-32213547-T-C		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GAREM1	protein_coding	protein_coding	ENST00000269209	6	345608

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.199	0.801	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	429	494	0.869	0.0000285	5692
Missense in Polyphen		138	194.81	0.7084		2139
Synonymous	-0.0835	202	201	1.01	0.0000124	1790
Loss of Function	4.04	8	33.1	0.242	0.00000211	374

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000476	0.0000462
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1: Acts as an adapter protein that plays a role in intracellular signaling cascades triggered either by the cell surface activated epidermal growth factor receptor and/or cytoplasmic protein tyrosine kinases. Promotes activation of the MAPK/ERK signaling pathway. Plays a role in the regulation of cell proliferation. {ECO:0000269|PubMed:19509291}.
• Pathway: EGFR1 (Consensus)

Intolerance Scores

• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.2

Haploinsufficiency Scores

• pHI: 0.553
• hipred: Y
• hipred_score: 0.543
• ghis: 0.507

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Garem1

Gene ontology

• Biological process: epidermal growth factor receptor signaling pathway;positive regulation of cell population proliferation;positive regulation of cell division;positive regulation of ERK1 and ERK2 cascade;cellular response to epidermal growth factor stimulus
• Cellular component: plasma membrane
• Molecular function: protein binding;proline-rich region binding