TBC1D21

TBC1 domain family member 21

Basic information

Region (hg38): 15:73873564-73889214

Links

ENSG00000167139 ∙ NCBI:161514 ∙ ∙ HGNC:28536 ∙ Uniprot:Q8IYX1 ∙ 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 TBC1D21 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D21 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	1		17
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	1	0

Variants in TBC1D21

This is a list of pathogenic ClinVar variants found in the TBC1D21 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-73881430-A-G		not specified	Uncertain significance (Sep 27, 2022)
15-73881474-C-T		not specified	Uncertain significance (May 30, 2024)
15-73881475-G-A		not specified	Uncertain significance (May 14, 2024)
15-73881659-G-A		not specified	Uncertain significance (Jun 05, 2023)
15-73881663-G-C		not specified	Uncertain significance (Jul 19, 2023)
15-73881672-C-T		not specified	Uncertain significance (Mar 19, 2024)
15-73881687-C-T		not specified	Uncertain significance (May 26, 2024)
15-73881729-C-T		not specified	Uncertain significance (Dec 15, 2022)
15-73884180-A-G		not specified	Uncertain significance (Oct 10, 2023)
15-73884215-C-T		not specified	Uncertain significance (May 26, 2023)
15-73884784-G-A		not specified	Likely benign (Dec 13, 2022)
15-73884825-G-A		not specified	Uncertain significance (Sep 17, 2021)
15-73884873-G-A		not specified	Uncertain significance (Oct 26, 2022)
15-73886571-C-T		not specified	Uncertain significance (Jul 26, 2022)
15-73886575-C-G		not specified	Uncertain significance (Aug 22, 2023)
15-73887707-G-A		not specified	Uncertain significance (Dec 21, 2022)
15-73887719-G-A		not specified	Uncertain significance (Apr 25, 2023)
15-73887735-T-C		not specified	Uncertain significance (Mar 28, 2024)
15-73888434-G-A		not specified	Uncertain significance (Oct 26, 2021)
15-73888448-G-A		not specified	Uncertain significance (Jul 16, 2021)
15-73888478-G-A		not specified	Uncertain significance (Feb 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D21	protein_coding	protein_coding	ENST00000300504	11	15607

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.16e-7	0.784	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.486	175	194	0.902	0.0000109	2252
Missense in Polyphen		55	65.827	0.83553		822
Synonymous	0.456	71	76.1	0.934	0.00000460	578
Loss of Function	1.36	13	19.5	0.667	8.31e-7	220

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000799	0.000796
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.0000879
Middle Eastern	0.000217	0.000217
South Asian	0.0000981	0.0000980
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a GTPase-activating protein for Rab family protein(s) (PubMed:19077034). May be involved in acrosome formation and cytoskeletal reorganization during spermiogenesis, possibly by regulating RAB3A activity (PubMed:21128978). {ECO:0000305|PubMed:19077034, ECO:0000305|PubMed:21128978}.

Intolerance Scores

• loftool: 0.689
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.77

Haploinsufficiency Scores

• pHI: 0.235
• hipred: N
• hipred_score: 0.371
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0222

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d21

Gene ontology

• Biological process: intracellular protein transport;spermatogenesis;cell differentiation;activation of GTPase activity;regulation of cilium assembly
• Cellular component: acrosomal vesicle;cytoskeleton;extracellular exosome
• Molecular function: actin binding;GTPase activator activity;Rab GTPase binding