RAB19

RAB19, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 7:140404058-140427974

Links

ENSG00000146955 ∙ NCBI:401409 ∙ ∙ HGNC:19982 ∙ Uniprot:A4D1S5 ∙ 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 RAB19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB19 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in RAB19

This is a list of pathogenic ClinVar variants found in the RAB19 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-140407691-C-A		not specified	Uncertain significance (Dec 21, 2023)
7-140407795-T-C		not specified	Uncertain significance (Feb 05, 2024)
7-140407812-G-A		not specified	Uncertain significance (Jan 19, 2022)
7-140407829-T-G		not specified	Uncertain significance (Jun 11, 2024)
7-140411904-C-T		not specified	Uncertain significance (Mar 30, 2024)
7-140411952-A-G		not specified	Uncertain significance (Apr 23, 2024)
7-140411973-C-T		not specified	Uncertain significance (Jan 31, 2022)
7-140411974-G-A		not specified	Uncertain significance (Feb 16, 2023)
7-140411976-C-T		not specified	Uncertain significance (Dec 13, 2022)
7-140411977-G-T		not specified	Uncertain significance (May 30, 2024)
7-140411980-C-T		not specified	Uncertain significance (Feb 05, 2024)
7-140411983-C-T		not specified	Uncertain significance (Jun 22, 2023)
7-140411988-G-A		not specified	Uncertain significance (Feb 28, 2023)
7-140412003-T-C		Non-syndromic syndactyly	Uncertain significance (Oct 20, 2022)
7-140412028-G-C		not specified	Uncertain significance (Feb 12, 2024)
7-140425909-G-A		not specified	Uncertain significance (Dec 09, 2023)
7-140425926-G-A		not specified	Uncertain significance (May 25, 2022)
7-140425953-G-A		not specified	Uncertain significance (Jan 30, 2024)
7-140426038-C-T		not specified	Uncertain significance (Jun 10, 2024)
7-140426069-T-G		not specified	Uncertain significance (May 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB19	protein_coding	protein_coding	ENST00000537763	3	22208

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000158	0.134	125568	0	180	125748	0.000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.376	126	138	0.910	0.00000890	1428
Missense in Polyphen		54	56.169	0.96139		568
Synonymous	-0.489	60	55.4	1.08	0.00000359	424
Loss of Function	-0.557	8	6.47	1.24	2.73e-7	81

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000627	0.000627
Ashkenazi Jewish	0.00	0.00
East Asian	0.00821	0.00824
Finnish	0.00	0.00
European (Non-Finnish)	0.0000791	0.0000791
Middle Eastern	0.00821	0.00824
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Post-translational protein modification;Metabolism of proteins;RAB geranylgeranylation (Consensus)

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.517
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.212
• hipred: N
• hipred_score: 0.219
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.273

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab19
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; vision/eye phenotype; immune system phenotype

Gene ontology

• Biological process: intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;Rab protein signal transduction
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;plasma membrane;extracellular exosome
• Molecular function: GTPase activity;GTP binding