GARIN5A

golgi associated RAB2 interactor 5A

Basic information

Region (hg38): 19:50466785-50476848

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.

• not_specified (48 variants)
• not_provided (3 variants)

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. These statistics are base on transcript: NM_001308429.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			48	1		49
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	48	3	0

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