TBC1D28

TBC1 domain family member 28

Basic information

Region (hg38): 17:18634247-18644427

Links

ENSG00000189375 ∙ NCBI:254272 ∙ ∙ HGNC:26858 ∙ Uniprot:Q2M2D7 ∙ 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 TBC1D28 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D28 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in TBC1D28

This is a list of pathogenic ClinVar variants found in the TBC1D28 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-18636481-C-G		not specified	Uncertain significance (Aug 02, 2021)
17-18636491-C-T		not specified	Uncertain significance (Aug 13, 2021)
17-18636568-G-A		not specified	Uncertain significance (Aug 11, 2022)
17-18636593-G-C		not specified	Uncertain significance (Nov 08, 2021)
17-18636595-T-G		not specified	Uncertain significance (Nov 08, 2021)
17-18637871-C-T		not specified	Uncertain significance (Dec 08, 2021)
17-18637907-T-C		not specified	Uncertain significance (Dec 15, 2023)
17-18637958-C-T		not specified	Uncertain significance (Feb 13, 2024)
17-18637966-T-G		not specified	Uncertain significance (Dec 01, 2022)
17-18638354-C-G		not specified	Uncertain significance (Feb 07, 2023)
17-18638647-A-G		not specified	Uncertain significance (Jan 26, 2023)
17-18638669-C-G		not specified	Uncertain significance (Oct 12, 2022)
17-18638680-G-A		not specified	Likely benign (Jun 07, 2024)
17-18638694-C-A		not specified	Uncertain significance (Aug 04, 2023)
17-18638696-T-A		not specified	Uncertain significance (Dec 03, 2021)
17-18639192-T-C		not specified	Uncertain significance (Dec 28, 2023)
17-18641097-C-T		not specified	Uncertain significance (Apr 27, 2023)
17-18641303-T-C		not specified	Uncertain significance (Sep 28, 2022)
17-18641334-G-A		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D28	protein_coding	protein_coding	ENST00000345096	7	26945

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.61e-8	0.0666	124863	1	397	125261	0.00159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.284	122	113	1.08	0.00000641	1360
Missense in Polyphen		19	20.187	0.94118		279
Synonymous	-0.523	49	44.6	1.10	0.00000260	383
Loss of Function	-0.509	11	9.32	1.18	3.93e-7	127

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000531	0.000530
Ashkenazi Jewish	0.0222	0.0224
East Asian	0.00539	0.00535
Finnish	0.00	0.00
European (Non-Finnish)	0.000338	0.000335
Middle Eastern	0.00539	0.00535
South Asian	0.000295	0.000294
Other	0.00215	0.00214

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.773
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.366
• hipred: N
• hipred_score: 0.139
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: intracellular protein transport;activation of GTPase activity
• Cellular component: cell
• Molecular function: GTPase activator activity;Rab GTPase binding