GARIN4

golgi associated RAB2 interactor family member 4

Basic information

Region (hg38): 1:212624474-212626775

Previous symbols: [ "FAM71A" ]

Links

ENSG00000162771 ∙ NCBI:149647 ∙ OMIM:619852 ∙ HGNC:26541 ∙ Uniprot:Q8IYT1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GARIN4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GARIN4 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					2	2
missense			43	3		46
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	4	2

Variants in GARIN4

This is a list of pathogenic ClinVar variants found in the GARIN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-212624887-G-T		not specified	Uncertain significance (Nov 08, 2021)
1-212624899-C-T		not specified	Uncertain significance (Mar 29, 2022)
1-212624945-C-T		not specified	Uncertain significance (Sep 20, 2023)
1-212624978-A-C		not specified	Uncertain significance (May 05, 2023)
1-212624987-A-G		not specified	Uncertain significance (Feb 14, 2024)
1-212625008-C-T		not specified	Uncertain significance (Feb 13, 2024)
1-212625022-G-A		not specified	Uncertain significance (Nov 03, 2022)
1-212625056-T-C		not specified	Uncertain significance (Feb 28, 2024)
1-212625100-C-A		not specified	Likely benign (Feb 16, 2023)
1-212625114-C-G		not specified	Uncertain significance (Jun 01, 2023)
1-212625128-A-G		not specified	Uncertain significance (Jan 04, 2022)
1-212625135-G-T		not specified	Uncertain significance (Apr 25, 2023)
1-212625158-G-A		not specified	Uncertain significance (Jun 10, 2024)
1-212625199-A-G		not specified	Uncertain significance (Jan 29, 2024)
1-212625202-A-G		not specified	Uncertain significance (Feb 14, 2023)
1-212625205-C-T		not specified	Uncertain significance (Sep 22, 2022)
1-212625212-C-A		not specified	Uncertain significance (Jun 10, 2022)
1-212625224-T-C		not specified	Uncertain significance (Nov 06, 2023)
1-212625260-G-A		not specified	Uncertain significance (Jun 07, 2024)
1-212625355-C-G		not specified	Uncertain significance (Mar 20, 2023)
1-212625359-A-C		not specified	Uncertain significance (Sep 27, 2021)
1-212625391-T-G		not specified	Uncertain significance (Aug 02, 2021)
1-212625413-A-G		not specified	Uncertain significance (Apr 26, 2024)
1-212625489-C-G		not specified	Uncertain significance (Feb 10, 2023)
1-212625520-G-A		not specified	Uncertain significance (Oct 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GARIN4	protein_coding	protein_coding	ENST00000294829	1	2332

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.280	373	358	1.04	0.0000205	3897
Missense in Polyphen		64	68.918	0.92865		867
Synonymous	-0.130	144	142	1.01	0.00000873	1251
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.944
• rvis_EVS: 1.89
• rvis_percentile_EVS: 97.33

Haploinsufficiency Scores

• pHI: 0.155
• hipred: N
• hipred_score: 0.112
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00850

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam71a

Gene ontology

• Cellular component: nucleus