GARIN3

golgi associated RAB2B interactor family member 3

Basic information

Region (hg38): 5:157161845-157166264

Previous symbols: [ "FAM71B" ]

Links

ENSG00000170613 ∙ NCBI:153745 ∙ OMIM:619883 ∙ HGNC:28397 ∙ Uniprot:Q8TC56 ∙ 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 GARIN3 gene.

• Inborn genetic diseases (15 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GARIN3 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			14	2		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	2	0

Variants in GARIN3

This is a list of pathogenic ClinVar variants found in the GARIN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-157162458-T-C		not specified	Uncertain significance (Aug 08, 2023)
5-157162481-G-A		not specified	Likely benign (Jan 03, 2024)
5-157162508-A-G		not specified	Uncertain significance (Dec 15, 2022)
5-157162559-T-G		not specified	Uncertain significance (Apr 13, 2023)
5-157162597-T-G		not specified	Uncertain significance (Feb 06, 2024)
5-157162626-A-G		not specified	Uncertain significance (Feb 21, 2024)
5-157162649-C-T			Likely benign (Apr 01, 2024)
5-157162671-T-A		not specified	Uncertain significance (Dec 12, 2023)
5-157162704-C-G		not specified	Uncertain significance (Aug 01, 2022)
5-157162769-C-A		not specified	Uncertain significance (Jan 23, 2024)
5-157162804-G-T		not specified	Uncertain significance (Oct 19, 2021)
5-157162899-T-C		not specified	Uncertain significance (Aug 01, 2022)
5-157162900-C-G		not specified	Uncertain significance (Oct 04, 2022)
5-157162925-C-A		not specified	Uncertain significance (Jul 19, 2022)
5-157163061-A-C		not specified	Uncertain significance (Dec 08, 2023)
5-157163064-T-C		not specified	Uncertain significance (Feb 26, 2024)
5-157163087-G-T		not specified	Uncertain significance (Oct 02, 2023)
5-157163226-C-T		not specified	Uncertain significance (Dec 18, 2023)
5-157163239-G-T		not specified	Uncertain significance (Apr 25, 2023)
5-157163246-C-A		not specified	Uncertain significance (Nov 09, 2023)
5-157163256-A-T		not specified	Uncertain significance (Oct 06, 2022)
5-157163261-T-C		not specified	Likely benign (Sep 21, 2023)
5-157163273-G-A		not specified	Uncertain significance (Aug 13, 2021)
5-157163354-G-A		not specified	Uncertain significance (Apr 07, 2023)
5-157163403-C-T		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GARIN3	protein_coding	protein_coding	ENST00000302938	2	4419

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00217	0.770	125731	0	16	125747	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0585	333	336	0.991	0.0000196	3942
Missense in Polyphen		55	69.105	0.79589		926
Synonymous	-0.0802	133	132	1.01	0.00000839	1245
Loss of Function	0.957	5	7.90	0.633	5.22e-7	87

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.000326	0.000326
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in RNA biogenesis. {ECO:0000269|PubMed:17103222}.

Recessive Scores

• pRec: 0.0742

Intolerance Scores

• loftool: 0.641
• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.55

Haploinsufficiency Scores

• pHI: 0.0734
• hipred: N
• hipred_score: 0.158
• ghis: 0.389

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0500

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam71b

Gene ontology

• Cellular component: nucleus