TBCCD1

TBCC domain containing 1

Basic information

Region (hg38): 3:186546067-186570543

Links

ENSG00000113838 ∙ NCBI:55171 ∙ OMIM:619848 ∙ HGNC:25546 ∙ Uniprot:Q9NVR7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TBCCD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBCCD1 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					1	1
missense			29	2		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	2	1

Variants in TBCCD1

This is a list of pathogenic ClinVar variants found in the TBCCD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-186551192-G-C		not specified	Uncertain significance (Jun 29, 2022)
3-186551263-A-T		not specified	Uncertain significance (Nov 08, 2021)
3-186554314-C-A		not specified	Uncertain significance (Apr 16, 2024)
3-186554348-C-T		not specified	Uncertain significance (Feb 01, 2023)
3-186554367-C-T			Benign (Jul 18, 2018)
3-186554432-T-C		not specified	Uncertain significance (Sep 13, 2023)
3-186554435-T-C		not specified	Uncertain significance (Apr 16, 2024)
3-186554506-G-A		not specified	Uncertain significance (Jan 10, 2022)
3-186554587-C-T		not specified	Uncertain significance (Nov 08, 2022)
3-186554588-G-A		not specified	Uncertain significance (Apr 25, 2022)
3-186554720-T-C		not specified	Uncertain significance (Jan 23, 2023)
3-186554928-T-C		not specified	Uncertain significance (Apr 07, 2023)
3-186554938-G-A		not specified	Uncertain significance (Dec 07, 2021)
3-186554975-G-T		not specified	Uncertain significance (Dec 09, 2023)
3-186554976-C-G		not specified	Uncertain significance (Dec 09, 2023)
3-186555048-T-C		not specified	Uncertain significance (Jun 03, 2024)
3-186556540-C-T		not specified	Uncertain significance (Oct 27, 2023)
3-186556643-C-G		not specified	Uncertain significance (Mar 23, 2023)
3-186556645-G-A		not specified	Uncertain significance (Apr 12, 2023)
3-186556651-C-T		not specified	Uncertain significance (Dec 28, 2023)
3-186556654-G-A		not specified	Uncertain significance (May 06, 2022)
3-186556669-T-C		not specified	Uncertain significance (Jul 12, 2022)
3-186556700-T-G		not specified	Uncertain significance (Dec 06, 2021)
3-186556741-T-C		not specified	Likely benign (Feb 07, 2023)
3-186556751-C-T		not specified	Uncertain significance (Oct 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBCCD1	protein_coding	protein_coding	ENST00000424280	6	24471

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00198	0.997	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.699	269	303	0.887	0.0000154	3653
Missense in Polyphen		66	81.907	0.80579		968
Synonymous	-0.0128	114	114	1.00	0.00000609	1099
Loss of Function	2.91	9	24.6	0.366	0.00000130	274

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.000696	0.000695
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000164	0.000163
South Asian	0.000588	0.000588
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the regulation of centrosome and Golgi apparatus positioning, with consequences on cell shape and cell migration. {ECO:0000269|PubMed:20168327}.

Recessive Scores

• pRec: 0.157

Intolerance Scores

• loftool: 0.166
• rvis_EVS: -0.93
• rvis_percentile_EVS: 9.55

Haploinsufficiency Scores

• pHI: 0.178
• hipred: N
• hipred_score: 0.443
• ghis: 0.634

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0583

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbccd1
• Phenotype: hearing/vestibular/ear phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: cell morphogenesis;regulation of cell shape;regulation of cell migration;maintenance of centrosome location;maintenance of Golgi location
• Cellular component: cytoplasm;spindle pole centrosome