TBC1D22A

TBC1 domain family member 22A

Basic information

Region (hg38): 22:46762617-47175699

Previous symbols: [ "C22orf4" ]

Links

ENSG00000054611 ∙ NCBI:25771 ∙ OMIM:616879 ∙ HGNC:1309 ∙ Uniprot:Q8WUA7 ∙ 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 TBC1D22A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D22A 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			29		2	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	29	0	3

Variants in TBC1D22A

This is a list of pathogenic ClinVar variants found in the TBC1D22A region.

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

Position	Type	Phenotype	Significance	ClinVar
22-46792525-A-G		not specified	Uncertain significance (Feb 15, 2023)
22-46793530-C-G		not specified	Uncertain significance (May 26, 2024)
22-46793538-G-A		not specified	Uncertain significance (Oct 27, 2022)
22-46793667-G-A		not specified	Uncertain significance (May 28, 2024)
22-46793671-C-T		not specified	Uncertain significance (Dec 06, 2021)
22-46793704-G-A		not specified	Uncertain significance (Jun 07, 2023)
22-46793719-C-T			Benign (Mar 29, 2018)
22-46793781-C-A		not specified	Uncertain significance (Mar 02, 2023)
22-46793782-C-G		not specified	Uncertain significance (Sep 29, 2022)
22-46793784-A-G		not specified	Uncertain significance (Jan 29, 2024)
22-46793809-C-T		not specified	Uncertain significance (Feb 06, 2024)
22-46793850-G-C			Benign (Apr 25, 2018)
22-46797447-G-T		not specified	Uncertain significance (Jan 31, 2024)
22-46797452-A-T		not specified	Uncertain significance (Mar 20, 2024)
22-46797455-G-A		not specified	Uncertain significance (Jul 27, 2022)
22-46797461-G-A		not specified	Uncertain significance (Dec 01, 2022)
22-46797495-C-T		not specified	Uncertain significance (Dec 09, 2023)
22-46797507-C-T			Benign (Mar 29, 2018)
22-46797518-A-G		not specified	Uncertain significance (Jun 11, 2021)
22-46797549-C-T		not specified	Uncertain significance (Jun 09, 2022)
22-46797588-A-G		not specified	Uncertain significance (Jun 29, 2022)
22-46891317-C-G		not specified	Uncertain significance (Feb 11, 2022)
22-46894788-A-G		not specified	Uncertain significance (Apr 29, 2024)
22-46894809-G-A		not specified	Uncertain significance (May 18, 2023)
22-46894823-A-G		not specified	Uncertain significance (Aug 04, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D22A	protein_coding	protein_coding	ENST00000337137	13	412819

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.419	0.581	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	268	329	0.814	0.0000213	3410
Missense in Polyphen		92	147.73	0.62275		1571
Synonymous	-1.00	158	143	1.11	0.0000107	977
Loss of Function	3.76	6	27.1	0.221	0.00000126	307

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000618	0.0000615
Middle Eastern	0.0000545	0.0000544
South Asian	0.000167	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a GTPase-activating protein for Rab family protein(s). {ECO:0000250}.

Recessive Scores

• pRec: 0.0965

Intolerance Scores

• loftool: 0.493
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.43

Haploinsufficiency Scores

• pHI: 0.171
• hipred: Y
• hipred_score: 0.728
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.868

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d22a
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: intracellular protein transport;activation of GTPase activity;regulation of cilium assembly
• Cellular component: cell
• Molecular function: GTPase activator activity;protein binding;Rab GTPase binding;protein homodimerization activity;14-3-3 protein binding