GARRE1

granule associated Rac and RHOG effector 1

Basic information

Region (hg38): 19:34254551-34355566

Previous symbols: [ "KIAA0355" ]

Links

ENSG00000166398 ∙ NCBI:9710 ∙ OMIM:619335 ∙ HGNC:29016 ∙ Uniprot:O15063 ∙ 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 GARRE1 gene.

• Inborn genetic diseases (18 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GARRE1 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				5		5
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	5	0

Variants in GARRE1

This is a list of pathogenic ClinVar variants found in the GARRE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-34300519-C-T		not specified	Uncertain significance (Apr 28, 2023)
19-34300571-C-T		not specified	Uncertain significance (Sep 17, 2021)
19-34300581-G-A			Likely benign (Apr 01, 2022)
19-34300589-G-A		not specified	Uncertain significance (Nov 03, 2023)
19-34300669-G-A		not specified	Uncertain significance (Jun 29, 2022)
19-34300738-G-A		not specified	Uncertain significance (Oct 26, 2022)
19-34300826-A-G		not specified	Uncertain significance (Jan 08, 2024)
19-34300858-A-T		not specified	Uncertain significance (Oct 19, 2021)
19-34300861-C-T		not specified	Uncertain significance (Apr 22, 2022)
19-34300862-G-A		not specified	Uncertain significance (Mar 29, 2023)
19-34319917-G-A		not specified	Uncertain significance (Apr 07, 2022)
19-34319959-C-A		not specified	Uncertain significance (Dec 15, 2022)
19-34319981-G-T		not specified	Uncertain significance (Feb 22, 2023)
19-34320015-G-A		not specified	Uncertain significance (Mar 01, 2024)
19-34320034-G-A		not specified	Uncertain significance (Jan 16, 2024)
19-34327446-G-C		not specified	Uncertain significance (May 03, 2023)
19-34327452-A-T		not specified	Uncertain significance (Feb 05, 2024)
19-34327804-T-C		not specified	Uncertain significance (Jul 20, 2021)
19-34327825-G-A		not specified	Uncertain significance (Oct 27, 2022)
19-34328000-G-C		not specified	Uncertain significance (Nov 29, 2023)
19-34328004-G-T		not specified	Uncertain significance (Apr 24, 2023)
19-34328007-G-A			Likely benign (Oct 01, 2022)
19-34328031-G-T		not specified	Uncertain significance (May 09, 2022)
19-34328053-C-G		not specified	Uncertain significance (Dec 08, 2023)
19-34328107-G-A		not specified	Uncertain significance (Aug 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GARRE1	protein_coding	protein_coding	ENST00000299505	13	101050

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.973	0.0271	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.64	507	622	0.815	0.0000359	6982
Missense in Polyphen		218	306.76	0.71065		3589
Synonymous	-0.857	272	255	1.07	0.0000166	2159
Loss of Function	5.22	8	46.4	0.172	0.00000226	507

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000968	0.0000924
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000163	0.000163
South Asian	0.000229	0.000229
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.0566
• rvis_EVS: -1.12
• rvis_percentile_EVS: 6.61

Haploinsufficiency Scores

• pHI: 0.174
• hipred: N
• hipred_score: 0.492
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.197

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: 4931406P16Rik