GARIN5A

golgi associated RAB2 interactor 5A

Basic information

Region (hg38): 19:50466784-50476848

Previous symbols: [ "FAM71E1" ]

Links

ENSG00000142530 ∙ NCBI:112703 ∙ OMIM:619890 ∙ HGNC:25107 ∙ Uniprot:Q6IPT2 ∙ 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 GARIN5A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GARIN5A 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		1	2	3		6
Total	0	1	19	4	0

Variants in GARIN5A

This is a list of pathogenic ClinVar variants found in the GARIN5A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-50467630-C-G		not specified	Uncertain significance (May 27, 2022)
19-50467635-G-A		not specified	Uncertain significance (Jan 04, 2024)
19-50467666-G-A		not specified	Uncertain significance (Dec 15, 2022)
19-50467683-C-T		not specified	Uncertain significance (Aug 12, 2021)
19-50467687-C-T		not specified	Uncertain significance (May 24, 2024)
19-50467695-C-T		not specified	Uncertain significance (Mar 31, 2022)
19-50467696-C-T		not specified	Uncertain significance (Apr 19, 2023)
19-50467749-C-T		not specified	Uncertain significance (Jan 07, 2022)
19-50475344-C-T		not specified	Uncertain significance (Feb 09, 2023)
19-50475382-G-A		not specified	Uncertain significance (Aug 12, 2021)
19-50475400-C-T		not specified	Uncertain significance (Oct 12, 2022)
19-50475452-T-A		not specified	Uncertain significance (Sep 12, 2023)
19-50475477-C-T			Likely benign (May 01, 2022)
19-50475859-G-C		not specified	Uncertain significance (Jan 04, 2022)
19-50475885-C-T		not specified	Uncertain significance (Mar 25, 2024)
19-50476141-C-G		not specified	Uncertain significance (Nov 15, 2023)
19-50476279-T-C		not specified	Uncertain significance (Sep 06, 2022)
19-50476316-G-A		not specified	Uncertain significance (Jan 02, 2024)
19-50476319-G-A		not specified	Uncertain significance (Mar 20, 2024)
19-50476348-G-A		not specified	Uncertain significance (Nov 08, 2022)
19-50476351-G-A		not specified	Uncertain significance (Aug 22, 2023)
19-50476367-C-G		not specified	Uncertain significance (Mar 19, 2024)
19-50476539-G-C			Likely benign (Dec 01, 2023)
19-50476607-GC-G		Neurodevelopmental disorder with dysmorphic facies and variable seizures	Pathogenic (Sep 06, 2022)
19-50476608-C-T		Inborn genetic diseases	Uncertain significance (Sep 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GARIN5A	protein_coding	protein_coding	ENST00000595790	4	9969

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000231	0.532	125427	2	227	125656	0.000912

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0369	158	157	1.01	0.0000105	1447
Missense in Polyphen		45	57.075	0.78844		536
Synonymous	0.309	64	67.2	0.952	0.00000442	502
Loss of Function	0.448	6	7.31	0.821	3.10e-7	86

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000672	0.000670
Ashkenazi Jewish	0.000797	0.000794
East Asian	0.0000544	0.0000544
Finnish	0.000371	0.000370
European (Non-Finnish)	0.00172	0.00170
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000666	0.0000653
Other	0.000654	0.000652

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.714
• rvis_EVS: 0.19
• rvis_percentile_EVS: 67.03

Haploinsufficiency Scores

• pHI: 0.182
• hipred: N
• hipred_score: 0.146
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.260

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam71e1