RAB34

RAB34, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 17:28714281-28718429

Links

∙ NCBI:83871 ∙ OMIM:610917 ∙ HGNC:16519 ∙ Uniprot:P0DI83, Q9BZG1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

orofaciodigital syndrome 20 (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Orofaciodigital syndrome 20	AR	Cardiovascular	Among other findings, the condition may include potentially occult cardiovascular and/or gastrointestinal anomalies, and awareness may enable surveillance, early diagnosis, and management	Cardiovascular; Craniofacial; Gastrointestinal; Musculoskeletal; Neurologic	37384395; 37619988

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RAB34 gene.

not_specified (26 variants)
Orofaciodigital_syndrome_20 (6 variants)
Jeune_thoracic_dystrophy (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB34 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000031934.6. 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	2 clinvar	1 clinvar	24 clinvar			27
nonsense		1 clinvar				1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	2	2	24	2	0

Highest pathogenic variant AF is 0.000016728769

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB34	protein_coding	protein_coding	ENST00000447716	11	4149

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.43e-7	0.871	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	137	177	0.772	0.00000927	2045
Missense in Polyphen		57	77.777	0.73287		912
Synonymous	1.09	60	71.8	0.836	0.00000399	617
Loss of Function	1.56	13	20.7	0.629	0.00000124	207

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000358	0.000358
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000204	0.000202
Middle Eastern	0.000272	0.000272
South Asian	0.000132	0.000131
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Post-translational protein modification;Metabolism of proteins;RAB geranylgeranylation (Consensus)

Recessive Scores

pRec: 0.143

Intolerance Scores

loftool: 0.968
rvis_EVS: -0.6
rvis_percentile_EVS: 17.75

Haploinsufficiency Scores

pHI: 0.495
hipred: N
hipred_score: 0.301
ghis: 0.623

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.623

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Rab34
Phenotype: craniofacial phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; digestive/alimentary phenotype; limbs/digits/tail phenotype; vision/eye phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Gene ontology

Biological process: intracellular protein transport;endocytosis;antigen processing and presentation;cell projection organization;lysosome localization;Rab protein signal transduction;Golgi to plasma membrane protein transport;macropinocytosis;positive regulation of smoothened signaling pathway;protein localization to plasma membrane;phagosome maturation;phagosome-lysosome fusion
Cellular component: Golgi apparatus;Golgi stack;cilium;phagocytic vesicle membrane;vesicle;Golgi cisterna;ruffle membrane;phagocytic vesicle;perinuclear region of cytoplasm;extracellular exosome
Molecular function: GTPase activity;protein binding;GTP binding;Ral GTPase binding;GTP-dependent protein binding