RAB3IP

RAB3A interacting protein

Basic information

Region (hg38): 12:69738859-69823204

Links

ENSG00000127328 ∙ NCBI:117177 ∙ OMIM:608686 ∙ HGNC:16508 ∙ Uniprot:Q96QF0 ∙ 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 RAB3IP gene.

• Inborn genetic diseases (22 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB3IP 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in RAB3IP

This is a list of pathogenic ClinVar variants found in the RAB3IP region.

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

Position	Type	Phenotype	Significance	ClinVar
12-69755384-G-A		not specified	Likely benign (Feb 28, 2024)
12-69755509-C-T		not specified	Likely benign (Mar 04, 2024)
12-69755521-G-A		not specified	Uncertain significance (Jan 03, 2024)
12-69755641-C-T		not specified	Uncertain significance (Dec 07, 2021)
12-69755649-T-C		not specified	Uncertain significance (Aug 03, 2022)
12-69756422-C-T		not specified	Uncertain significance (Dec 02, 2022)
12-69756434-C-T		not specified	Uncertain significance (Sep 17, 2021)
12-69756446-T-A		not specified	Uncertain significance (Feb 01, 2023)
12-69756584-G-A		not specified	Uncertain significance (Jun 06, 2023)
12-69756617-A-G		not specified	Uncertain significance (Oct 26, 2021)
12-69784766-G-A		not specified	Uncertain significance (Feb 23, 2023)
12-69794440-G-A		not specified	Uncertain significance (Oct 18, 2021)
12-69794455-A-G		not specified	Uncertain significance (Jun 01, 2023)
12-69794468-T-C		not specified	Uncertain significance (Feb 28, 2023)
12-69795302-G-T		not specified	Uncertain significance (Feb 01, 2023)
12-69795309-A-G		not specified	Uncertain significance (Jul 12, 2023)
12-69795337-G-A		not specified	Uncertain significance (Aug 02, 2021)
12-69800237-G-A		not specified	Uncertain significance (Jun 07, 2023)
12-69800333-G-T		not specified	Uncertain significance (Nov 21, 2022)
12-69801648-C-G		not specified	Uncertain significance (Jan 10, 2023)
12-69801681-C-T		not specified	Uncertain significance (Apr 28, 2022)
12-69801696-T-G		not specified	Uncertain significance (Aug 04, 2023)
12-69812855-T-G		not specified	Uncertain significance (Jul 26, 2021)
12-69812970-T-C		not specified	Uncertain significance (Jul 20, 2021)
12-69813026-G-C		not specified	Uncertain significance (Mar 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB3IP	protein_coding	protein_coding	ENST00000550536	11	84524

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.67e-8	0.960	125705	0	42	125747	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.670	219	249	0.880	0.0000124	3093
Missense in Polyphen		46	90.504	0.50826		1191
Synonymous	-1.44	108	90.6	1.19	0.00000463	893
Loss of Function	2.03	17	28.7	0.592	0.00000164	347

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000233	0.000233
Ashkenazi Jewish	0.00	0.00
East Asian	0.000286	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000196	0.000193
Middle Eastern	0.000286	0.000272
South Asian	0.000164	0.000163
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor (GEF) which may activate RAB8A and RAB8B. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP- bound form. Mediates the release of GDP from RAB8A and RAB8B but not from RAB3A or RAB5. Modulates actin organization and promotes polarized transport of RAB8A-specific vesicles to the cell surface. Together with RAB11A, RAB8A, the exocyst complex, PARD3, PRKCI, ANXA2, CDC42 and DNMBP promotes transcytosis of PODXL to the apical membrane initiation sites (AMIS), apical surface formation and lumenogenesis. {ECO:0000269|PubMed:12221131, ECO:0000269|PubMed:20890297, ECO:0000269|PubMed:20937701}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs;Anchoring of the basal body to the plasma membrane;VxPx cargo-targeting to cilium;BBSome-mediated cargo-targeting to cilium;Cargo trafficking to the periciliary membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.328
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.0597
• hipred: N
• hipred_score: 0.369
• ghis: 0.608

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: Rab3ip
• Phenotype: homeostasis/metabolism phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); normal phenotype

Zebrafish Information Network

• Gene name: rab3ip
• Affected structure: Kupffer's vesicle
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: protein targeting to membrane;ciliary basal body-plasma membrane docking
• Cellular component: nucleus;cytosol;cytoskeleton;lamellipodium
• Molecular function: protein binding;Rab guanyl-nucleotide exchange factor activity