GARIN6

golgi associated RAB2 interactor family member 6

Basic information

Region (hg38): 12:99647752-99650114

Previous symbols: [ "FAM71C" ]

Links

ENSG00000180219 ∙ NCBI:196472 ∙ ∙ HGNC:28594 ∙ Uniprot:Q8NEG0 ∙ 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 GARIN6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GARIN6 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			13	3	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	3	1

Variants in GARIN6

This is a list of pathogenic ClinVar variants found in the GARIN6 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-99648206-C-T		not specified	Uncertain significance (Oct 12, 2021)
12-99648218-G-A		not specified	Uncertain significance (Nov 22, 2021)
12-99648277-G-A		not specified	Uncertain significance (Jul 27, 2022)
12-99648308-T-C		not specified	Uncertain significance (May 15, 2024)
12-99648353-T-C		not specified	Uncertain significance (Jan 03, 2022)
12-99648357-C-A		not specified	Uncertain significance (Mar 02, 2023)
12-99648394-G-A			Benign (Sep 01, 2022)
12-99648403-A-T		not specified	Uncertain significance (Aug 02, 2023)
12-99648443-G-A		not specified	Uncertain significance (May 16, 2022)
12-99648454-G-A		not specified	Likely benign (Jan 04, 2022)
12-99648554-A-G		not specified	Uncertain significance (Jul 12, 2022)
12-99648611-G-A		not specified	Uncertain significance (Sep 14, 2022)
12-99648662-T-C		not specified	Uncertain significance (Jun 22, 2023)
12-99648726-G-T		not specified	Uncertain significance (Jun 05, 2024)
12-99648749-T-C		not specified	Likely benign (Aug 30, 2021)
12-99648787-G-A		not specified	Uncertain significance (Jan 23, 2024)
12-99649318-G-A		not specified	Uncertain significance (Dec 05, 2022)
12-99649333-A-C		not specified	Likely benign (Mar 07, 2023)
12-99649346-T-A		not specified	Uncertain significance (Apr 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GARIN6	protein_coding	protein_coding	ENST00000324341	2	2294

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.167	0.778	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.402	152	139	1.10	0.00000793	1592
Missense in Polyphen		39	31.072	1.2552		406
Synonymous	-0.623	59	53.2	1.11	0.00000334	464
Loss of Function	1.58	2	6.25	0.320	4.50e-7	70

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

Recessive Scores

• pRec: 0.0935

Intolerance Scores

• loftool: 0.770
• rvis_EVS: 1.19
• rvis_percentile_EVS: 92.89

Haploinsufficiency Scores

• pHI: 0.0518
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.252

Gene Damage Prediction

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

Gene ontology

• Molecular function: protein binding