TBCCD1

protein-coding

TBCC domain containing 1

Gene summary

Involved in several processes, including maintenance of Golgi location; maintenance of centrosome location; and regulation of cell shape. Located in spindle pole centrosome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_018138.5

Inheritance

ClinVar variants

U:81B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.37

Max pathogenic AF

—

Genomic locus

chr3:186,546,067-186,570,543

External References & Databases

Ensembl (ENSG00000113838)

Transcript & Mutation Effects

hg38 • Region Span ~24.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

male infertility with azoospermia or oligozoospermia due to single gene mutationMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0018393

Submitter: King Faisal Specialist Hospital and Research Center

Alhathal et al., 2020 (PMID: 32719396) reported a LOF variant in a large male infertility cohort (n=285 infertile man and case–control fertile man). Gene is scored according to ClinGen classification. Moderate with total score of 8. Single variant segregation (3 points), experimental evidence: Animal model (4 points) (Tbccd1tm1b(EUCOMM)Hmgu) and testicular expression (1 points) (PMID: 20168327).

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TBCCD1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 78

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018138.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar		1 clinvar	3
missense			78 clinvar	2 clinvar		80
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	81	2	1	84

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018138.5	RefSeq	NP_060608.1	6	MANE Select
ENST00000338733.10	Ensembl	ENSP00000341652.5	6	MANE Select
NM_001134415.1	RefSeq	NP_001127887.1	6	Standard
NM_001286749.2	RefSeq	NP_001273678.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000424280
Coding exons: 6
Length: 24471
Individuals with no LoFs: 125699
Homozygous LoFs: 0
Heterozygous LoFs: 49
Defined: 125748
p: 0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.699	269	303	0.887	0.0000154	3653
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0.00070	0.00069	rare
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.00059	0.00059	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0583

Gene Damage Prediction

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