RAB30

RAB30, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 11:82973133-83071923

Links

ENSG00000137502 ∙ NCBI:27314 ∙ OMIM:605693 ∙ HGNC:9770 ∙ Uniprot:Q15771 ∙ 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 RAB30 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB30 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in RAB30

This is a list of pathogenic ClinVar variants found in the RAB30 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-82982185-T-A		not specified	Uncertain significance (Sep 16, 2021)
11-82982197-T-C		not specified	Uncertain significance (Jul 29, 2023)
11-82982221-G-C		not specified	Uncertain significance (Dec 01, 2022)
11-82982340-A-G		not specified	Uncertain significance (Mar 24, 2023)
11-82982386-C-G		not specified	Uncertain significance (Jul 14, 2023)
11-82997264-G-C		not specified	Uncertain significance (Dec 07, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB30	protein_coding	protein_coding	ENST00000533486	4	98791

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.921	0.0786	125742	0	4	125746	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.94	54	112	0.484	0.00000579	1327
Missense in Polyphen		15	53.988	0.27784		634
Synonymous	0.690	35	40.6	0.862	0.00000210	382
Loss of Function	3.02	1	12.5	0.0797	8.73e-7	120

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)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different set of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion (By similarity). Required for maintaining the structural integrity of the Golgi apparatus, possibly by mediating interactions with cytoplasmic scaffolding proteins. {ECO:0000250, ECO:0000269|PubMed:22188167}.
• Pathway: miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Intra-Golgi traffic;RAB geranylgeranylation;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• pHI: 0.423
• hipred: Y
• hipred_score: 0.728
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.404

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab30

Gene ontology

• Biological process: intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;Golgi organization;Rab protein signal transduction
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;Golgi stack;cis-Golgi network;trans-Golgi network;Golgi cisterna;intracellular membrane-bounded organelle
• Molecular function: GTPase activity;GTP binding