TBC1D19

TBC1 domain family member 19

Basic information

Region (hg38): 4:26576437-26756223

Links

ENSG00000109680 ∙ NCBI:55296 ∙ ∙ HGNC:25624 ∙ Uniprot:Q8N5T2 ∙ 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 TBC1D19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D19 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in TBC1D19

This is a list of pathogenic ClinVar variants found in the TBC1D19 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-26584290-T-A		not specified	Uncertain significance (Apr 26, 2023)
4-26614408-G-A		not specified	Uncertain significance (Mar 07, 2023)
4-26620635-G-T		not specified	Uncertain significance (Nov 09, 2022)
4-26620649-A-C		not specified	Uncertain significance (Jun 21, 2023)
4-26637281-G-A		not specified	Uncertain significance (Jun 03, 2024)
4-26638784-A-G		not specified	Uncertain significance (Jul 12, 2023)
4-26638816-A-G		not specified	Uncertain significance (Feb 10, 2022)
4-26659612-C-T		not specified	Uncertain significance (Dec 17, 2023)
4-26659613-G-A		not specified	Uncertain significance (May 30, 2023)
4-26659621-A-G		not specified	Uncertain significance (Mar 07, 2024)
4-26659642-C-G		not specified	Uncertain significance (May 30, 2024)
4-26659642-C-T		not specified	Uncertain significance (Dec 13, 2022)
4-26666344-T-G		not specified	Uncertain significance (Oct 06, 2024)
4-26673803-C-T		not specified	Uncertain significance (Jun 30, 2022)
4-26673826-A-G		not specified	Uncertain significance (Sep 18, 2024)
4-26673836-C-A		not specified	Uncertain significance (Dec 09, 2023)
4-26673857-C-T		not specified	Uncertain significance (Oct 05, 2023)
4-26673883-C-T		not specified	Uncertain significance (Dec 04, 2024)
4-26735457-G-A		not specified	Uncertain significance (Aug 01, 2023)
4-26735482-T-C		not specified	Uncertain significance (Dec 03, 2024)
4-26754919-A-G		not specified	Uncertain significance (Sep 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D19	protein_coding	protein_coding	ENST00000264866	21	178915

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000631	0.999	125713	0	28	125741	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.85	178	262	0.679	0.0000129	3400
Missense in Polyphen		44	82.88	0.53089		1070
Synonymous	1.96	64	87.3	0.733	0.00000410	956
Loss of Function	3.88	13	39.2	0.332	0.00000211	466

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000314	0.0000314
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000544
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.0000557	0.0000544
South Asian	0.000309	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a GTPase-activating protein for Rab family protein(s).

Recessive Scores

• pRec: 0.121

Intolerance Scores

• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.99

Haploinsufficiency Scores

• pHI: 0.127
• hipred: N
• hipred_score: 0.488
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.275

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d19

Gene ontology

• Biological process: positive regulation of GTPase activity;regulation of cilium assembly
• Molecular function: GTPase activator activity;protein binding