RAB12

RAB12, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 18:8609437-8639383

Links

ENSG00000206418

∙ NCBI:201475 ∙ OMIM:616448 ∙ HGNC:31332 ∙ Uniprot:Q6IQ22 ∙ 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 RAB12 gene.

not_specified (21 variants)
RAB12-related_disorder (2 variants)
task-specific_movement_disorders (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB12 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001025300.3. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			20 clinvar			20
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	20	2	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB12	protein_coding	protein_coding	ENST00000329286	6	29937

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0428	0.932	124754	0	25	124779	0.000100

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.69	70	123	0.570	0.00000598	1595
Missense in Polyphen		12	35.342	0.33954		450
Synonymous	-1.11	57	47.3	1.21	0.00000249	458
Loss of Function	1.95	4	10.9	0.365	4.60e-7	149

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00110	0.00107
Ashkenazi Jewish	0.00	0.00
East Asian	0.000179	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000284	0.0000177
Middle Eastern	0.000179	0.000111
South Asian	0.0000743	0.0000327
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. That Rab may play a role in protein transport from recycling endosomes to lysosomes regulating, for instance, the degradation of the transferrin receptor. Involved in autophagy (By similarity). {ECO:0000250}.;
Pathway: Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs;RAB geranylgeranylation (Consensus)

Intolerance Scores

loftool: 0.106
rvis_EVS: -0.21
rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

pHI: 0.159
hipred: Y
hipred_score: 0.728
ghis: 0.649

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Rab12
Phenotype

Gene ontology

Biological process: intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;autophagy;endosome to lysosome transport;positive regulation of macroautophagy;Rab protein signal transduction;cellular protein catabolic process;cellular response to interferon-gamma
Cellular component: Golgi membrane;lysosome;lysosomal membrane;autophagosome;endoplasmic reticulum membrane;trans-Golgi network;cytosol;phagocytic vesicle;recycling endosome membrane
Molecular function: GTPase activity;protein binding;GTP binding;GDP binding