TBC1D32

TBC1 domain family member 32, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 6:121079494-121334745

Previous symbols: [ "C6orf171", "C6orf170" ]

Links

ENSG00000146350 ∙ NCBI:221322 ∙ OMIM:615867 ∙ HGNC:21485 ∙ Uniprot:Q96NH3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• orofaciodigital syndrome (Moderate), mode of inheritance: AR
• ciliopathy (Definitive), mode of inheritance: AR
• orofaciodigital syndrome IX (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TBC1D32 gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D32 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			2	20	10	32
missense			98	12	14	124
nonsense		3	2			5
start loss						0
frameshift	1		1			2
inframe indel			2			2
splice donor/acceptor (+/-2bp)		1				1
splice region			3	6	6	15
non coding				10	9	19
Total	1	4	105	42	33

Highest pathogenic variant AF is 0.00000658

Variants in TBC1D32

This is a list of pathogenic ClinVar variants found in the TBC1D32 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-121080796-C-T			Likely benign (Feb 01, 2023)
6-121080820-C-T		Inborn genetic diseases	Uncertain significance (Feb 28, 2023)
6-121080821-G-A		Joubert syndrome 36	Likely pathogenic (Mar 14, 2024)
6-121080832-T-C			Uncertain significance (Sep 26, 2022)
6-121080834-C-T			Uncertain significance (Feb 10, 2022)
6-121080850-T-G			Benign (Dec 21, 2023)
6-121080868-C-G			Uncertain significance (May 01, 2022)
6-121080878-G-A			Benign (Jan 22, 2024)
6-121090893-A-G			Uncertain significance (May 29, 2023)
6-121090931-G-C		Inborn genetic diseases	Uncertain significance (Jan 10, 2023)
6-121090932-A-C		TBC1D32-related disorder	Likely benign (Sep 13, 2022)
6-121090941-T-C		Microcephaly	Uncertain significance (-)
6-121090968-G-A			Benign (Jan 08, 2024)
6-121090980-T-C		Inborn genetic diseases	Uncertain significance (Jan 12, 2024)
6-121090997-A-G			Likely benign (Jul 19, 2018)
6-121091045-TA-T			Benign (Jul 17, 2023)
6-121091045-T-TA			Benign (Jan 29, 2024)
6-121091045-T-TAA			Benign (Jan 12, 2024)
6-121106042-G-A			Uncertain significance (Jun 22, 2023)
6-121106064-C-A		TBC1D32-related disorder	Likely benign (Sep 25, 2018)
6-121106064-C-T		Inborn genetic diseases	Uncertain significance (Nov 17, 2022)
6-121106104-G-T			Likely benign (May 04, 2022)
6-121106116-A-G			Likely benign (Dec 13, 2018)
6-121106137-T-C			Benign (Jan 24, 2024)
6-121106155-A-C			Benign (Oct 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D32	protein_coding	protein_coding	ENST00000398212	32	255252

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.00e-27	0.424	124391	0	404	124795	0.00162

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0369	622	625	0.996	0.0000297	8244
Missense in Polyphen		202	205.28	0.98402		2827
Synonymous	-1.26	237	214	1.11	0.00000991	2252
Loss of Function	2.23	52	72.5	0.718	0.00000352	963

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00154	0.00153
Ashkenazi Jewish	0.000204	0.000199
East Asian	0.00153	0.00150
Finnish	0.00896	0.00899
European (Non-Finnish)	0.00102	0.00101
Middle Eastern	0.00153	0.00150
South Asian	0.000574	0.000556
Other	0.00166	0.00165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for high-level Shh responses in the developing neural tube. Together with CDK20, controls the structure of the primary cilium by coordinating assembly of the ciliary membrane and axoneme, allowing GLI2 to be properly activated in response to Shh signaling (By similarity). {ECO:0000250}.

Intolerance Scores

• rvis_EVS: 1.7
• rvis_percentile_EVS: 96.43

Haploinsufficiency Scores

• pHI: 0.0770
• hipred: N
• hipred_score: 0.368
• ghis: 0.455

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d32
• Phenotype: growth/size/body region phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); craniofacial phenotype; vision/eye phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); pigmentation phenotype; embryo phenotype; respiratory system phenotype; immune system phenotype; renal/urinary system phenotype; digestive/alimentary phenotype; limbs/digits/tail phenotype

Zebrafish Information Network

• Gene name: tbc1d32
• Affected structure: renal tubule
• Phenotype tag: abnormal
• Phenotype quality: curled

Gene ontology

• Biological process: lens development in camera-type eye;retinal pigment epithelium development;determination of left/right symmetry;heart development;embryonic digit morphogenesis;cilium assembly;smoothened signaling pathway involved in dorsal/ventral neural tube patterning;protein localization to cilium;non-motile cilium assembly
• Cellular component: cytoplasm;cilium