RAB3IL1

RAB3A interacting protein like 1

Basic information

Region (hg38): 11:61897301-61920269

Links

ENSG00000167994 ∙ NCBI:5866 ∙ ∙ HGNC:9780 ∙ Uniprot:Q8TBN0 ∙ 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 RAB3IL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB3IL1 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			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	0

Variants in RAB3IL1

This is a list of pathogenic ClinVar variants found in the RAB3IL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-61898291-G-A		not specified	Uncertain significance (Oct 26, 2022)
11-61898317-C-T		not specified	Uncertain significance (Mar 31, 2023)
11-61902450-G-A		not specified	Uncertain significance (Sep 29, 2023)
11-61902492-G-A		not specified	Uncertain significance (Jun 02, 2023)
11-61902495-G-A		not specified	Uncertain significance (Dec 02, 2022)
11-61902506-C-T		not specified	Uncertain significance (May 31, 2023)
11-61904559-A-G		not specified	Uncertain significance (Nov 13, 2024)
11-61904591-G-A		not specified	Uncertain significance (Oct 13, 2023)
11-61904597-G-A		not specified	Uncertain significance (Aug 22, 2023)
11-61904637-C-T		not specified	Uncertain significance (Nov 29, 2021)
11-61904765-T-C		not specified	Uncertain significance (Sep 26, 2024)
11-61904766-G-C		not specified	Uncertain significance (Dec 13, 2022)
11-61906509-G-C		not specified	Uncertain significance (Dec 20, 2023)
11-61906519-C-A		not specified	Uncertain significance (Jun 22, 2021)
11-61906519-C-T		not specified	Uncertain significance (Nov 22, 2021)
11-61906539-G-A		not specified	Uncertain significance (Dec 28, 2023)
11-61906551-C-T		not specified	Uncertain significance (Apr 26, 2024)
11-61906552-G-A		not specified	Uncertain significance (Aug 12, 2021)
11-61906587-C-T		not specified	Uncertain significance (Mar 18, 2024)
11-61906614-T-C		not specified	Uncertain significance (Nov 25, 2024)
11-61906647-G-A		not specified	Uncertain significance (Mar 20, 2023)
11-61906663-C-T		not specified	Uncertain significance (Sep 16, 2021)
11-61906681-C-T		not specified	Uncertain significance (Oct 01, 2024)
11-61907400-C-T		not specified	Uncertain significance (Dec 28, 2023)
11-61907428-C-T		not specified	Uncertain significance (Oct 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB3IL1	protein_coding	protein_coding	ENST00000394836	10	22969

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000368	0.991	125727	0	12	125739	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.483	206	226	0.910	0.0000141	2403
Missense in Polyphen		68	85.996	0.79073		889
Synonymous	1.17	82	96.6	0.849	0.00000614	761
Loss of Function	2.30	9	20.1	0.447	0.00000117	220

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)	0.0000717	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.000108	0.0000980
Other	0.000184	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor (GEF) which may activate RAB3A, a GTPase that regulates synaptic vesicle exocytosis. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. May also activate RAB8A and RAB8B. {ECO:0000269|PubMed:20937701}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Recessive Scores

• pRec: 0.140

Intolerance Scores

• loftool: 0.675
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.73

Haploinsufficiency Scores

• pHI: 0.377
• hipred: N
• hipred_score: 0.411
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.732

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab3il1

Gene ontology

• Biological process: protein transport
• Cellular component: cytosol
• Molecular function: protein binding;Rab guanyl-nucleotide exchange factor activity