GARIN5B

golgi associated RAB2 interactor family member 5B

Basic information

Region (hg38): 19:55354908-55363260

Previous symbols: [ "C19orf16", "FAM71E2" ]

Links

ENSG00000180043 ∙ NCBI:284418 ∙ ∙ HGNC:25278 ∙ Uniprot:Q8N5Q1 ∙ 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 GARIN5B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GARIN5B 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				4		4
missense			107	7		114
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	107	11	0

Variants in GARIN5B

This is a list of pathogenic ClinVar variants found in the GARIN5B region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55355316-G-A		not specified	Likely benign (Mar 29, 2022)
19-55358156-G-T		not specified	Uncertain significance (Oct 03, 2022)
19-55358164-C-T		not specified	Uncertain significance (Jun 07, 2024)
19-55358169-G-A		not specified	Likely benign (Apr 05, 2023)
19-55358230-G-C		not specified	Uncertain significance (Oct 01, 2024)
19-55358232-A-G		not specified	Uncertain significance (Jun 22, 2024)
19-55358319-G-C		not specified	Uncertain significance (Jun 02, 2023)
19-55358319-G-T		not specified	Uncertain significance (Nov 12, 2024)
19-55358358-A-C		not specified	Uncertain significance (Apr 18, 2023)
19-55358362-G-A		not specified	Uncertain significance (May 04, 2023)
19-55358386-G-A		not specified	Uncertain significance (Apr 08, 2024)
19-55358400-G-A		not specified	Uncertain significance (Aug 28, 2024)
19-55358401-G-T		not specified	Uncertain significance (Nov 15, 2021)
19-55358419-T-C		not specified	Uncertain significance (Jan 27, 2025)
19-55358424-G-A		not specified	Uncertain significance (Jan 30, 2024)
19-55358466-T-C		not specified	Uncertain significance (Oct 04, 2022)
19-55358472-C-T		not specified	Uncertain significance (Sep 29, 2023)
19-55358540-C-A		not specified	Uncertain significance (Dec 16, 2024)
19-55358610-A-C		not specified	Uncertain significance (Sep 02, 2024)
19-55358617-T-G		not specified	Uncertain significance (Aug 17, 2022)
19-55358628-A-G		not specified	Likely benign (Mar 04, 2025)
19-55358641-C-A		not specified	Uncertain significance (Feb 21, 2024)
19-55358646-C-T		not specified	Likely benign (Jan 01, 2025)
19-55358691-G-A		not specified	Uncertain significance (Apr 24, 2024)
19-55358692-T-C		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GARIN5B	protein_coding	protein_coding	ENST00000424985	10	8353

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.57e-9	0.952	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	437	500	0.873	0.0000303	5797
Missense in Polyphen		42	54.717	0.76759		678
Synonymous	2.02	194	233	0.832	0.0000161	1994
Loss of Function	2.03	19	31.3	0.608	0.00000146	409

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.205

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.290

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam71e2