TBC1D12

TBC1 domain family member 12

Basic information

Region (hg38): 10:94402540-94536332

Links

ENSG00000108239 ∙ NCBI:23232 ∙ OMIM:620003 ∙ HGNC:29082 ∙ Uniprot:O60347 ∙ 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 TBC1D12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D12 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			39	1		40
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	2	0

Variants in TBC1D12

This is a list of pathogenic ClinVar variants found in the TBC1D12 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-94402704-A-G		not specified	Uncertain significance (Jan 22, 2024)
10-94402712-C-G		not specified	Uncertain significance (Mar 25, 2022)
10-94402755-C-T		not specified	Uncertain significance (Jun 16, 2024)
10-94402759-CGGAGGAGGCTGACGAGGA-C			Likely benign (Feb 01, 2023)
10-94402776-G-C		not specified	Uncertain significance (Jan 02, 2024)
10-94402791-G-A		not specified	Uncertain significance (Aug 15, 2023)
10-94402875-T-C		not specified	Uncertain significance (Jun 29, 2023)
10-94402906-C-G		not specified	Uncertain significance (Jun 06, 2023)
10-94402906-C-T		not specified	Uncertain significance (Nov 14, 2023)
10-94402938-T-C		not specified	Uncertain significance (May 30, 2024)
10-94402939-G-T		not specified	Uncertain significance (May 30, 2024)
10-94402963-A-T		not specified	Uncertain significance (Dec 07, 2021)
10-94402971-G-A		not specified	Uncertain significance (Sep 17, 2021)
10-94402980-G-A		not specified	Uncertain significance (May 31, 2024)
10-94402987-G-T		not specified	Uncertain significance (Dec 06, 2021)
10-94403035-T-A		not specified	Uncertain significance (Aug 12, 2021)
10-94403057-T-A		not specified	Uncertain significance (Sep 17, 2021)
10-94403100-T-G		not specified	Uncertain significance (Sep 17, 2021)
10-94403145-G-A		not specified	Uncertain significance (Dec 19, 2023)
10-94403176-C-T		not specified	Uncertain significance (Sep 06, 2022)
10-94403211-C-T		not specified	Uncertain significance (Aug 21, 2023)
10-94403239-C-T		not specified	Uncertain significance (Apr 07, 2022)
10-94403251-A-G		not specified	Uncertain significance (Sep 06, 2022)
10-94403269-C-T		not specified	Uncertain significance (Jan 09, 2024)
10-94403287-G-C		not specified	Uncertain significance (May 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D12	protein_coding	protein_coding	ENST00000225235	13	133427

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000172	1.00	124767	0	24	124791	0.0000962

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	305	369	0.827	0.0000188	4936
Missense in Polyphen		92	155.6	0.59126		2055
Synonymous	0.446	135	142	0.952	0.00000708	1528
Loss of Function	3.49	15	38.4	0.391	0.00000246	420

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000939	0.0000936
Ashkenazi Jewish	0.00	0.00
East Asian	0.000168	0.000167
Finnish	0.00	0.00
European (Non-Finnish)	0.0000888	0.0000883
Middle Eastern	0.000168	0.000167
South Asian	0.000272	0.000261
Other	0.000169	0.000165

dbNSFP

Source: dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.287
• hipred: Y
• hipred_score: 0.592
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.287

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d12

Gene ontology

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