GARIN1B

golgi associated RAB2 interactor 1B

Basic information

Region (hg38): 7:128709061-128731743

Previous symbols: [ "FAM137A", "FAM71F1" ]

Links

ENSG00000135248 ∙ NCBI:84691 ∙ OMIM:619905 ∙ HGNC:30704 ∙ Uniprot:Q96KD3 ∙ 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 GARIN1B gene.

• not_specified (34 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GARIN1B gene is commonly pathogenic or not. These statistics are base on transcript: NM_001282788.3. 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					1	1
missense			31	3		34
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	31	3	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GARIN1B	protein_coding	protein_coding	ENST00000315184	7	22683

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.05e-7	0.551	125494	2	251	125747	0.00101

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.782	155	185	0.838	0.00000956	2236
Missense in Polyphen		54	68.837	0.78446		858
Synonymous	0.672	71	78.6	0.904	0.00000440	685
Loss of Function	0.995	13	17.5	0.743	8.28e-7	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00425	0.00420
Ashkenazi Jewish	0.00	0.00
East Asian	0.000490	0.000489
Finnish	0.00453	0.00449
European (Non-Finnish)	0.000556	0.000554
Middle Eastern	0.000490	0.000489
South Asian	0.0000653	0.0000653
Other	0.00115	0.00114

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0867

Intolerance Scores

• loftool: 0.893
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.37

Haploinsufficiency Scores

• pHI: 0.0845
• hipred: N
• hipred_score: 0.155

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00460

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam71f1