TBC1D31

TBC1 domain family member 31, the group of WD repeat domain containing

Basic information

Region (hg38): 8:123041968-123152153

Previous symbols: [ "WDR67" ]

Links

ENSG00000156787 ∙ NCBI:93594 ∙ ∙ HGNC:30888 ∙ Uniprot:Q96DN5 ∙ 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 TBC1D31 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D31 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			59	9		68
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			1	1		2
Total	0	0	61	11	0

Variants in TBC1D31

This is a list of pathogenic ClinVar variants found in the TBC1D31 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-123041989-G-A		not specified	Uncertain significance (Jan 26, 2023)
8-123042022-A-T		not specified	Uncertain significance (Nov 09, 2021)
8-123042023-T-C		not specified	Uncertain significance (Oct 29, 2021)
8-123042073-T-C		not specified	Uncertain significance (May 11, 2022)
8-123072774-A-G		not specified	Uncertain significance (Feb 02, 2022)
8-123072785-C-G		not specified	Uncertain significance (Oct 06, 2021)
8-123072801-G-C		not specified	Uncertain significance (Apr 05, 2023)
8-123072840-G-A		not specified	Uncertain significance (Jun 13, 2024)
8-123077109-A-G		TBC1D31-related disorder	Uncertain significance (Jul 03, 2024)
8-123077127-A-G		not specified	Uncertain significance (Oct 29, 2021)
8-123077194-G-A		not specified	Uncertain significance (Feb 12, 2024)
8-123077220-C-G		Inherited genitourinary tract anomalies	Likely pathogenic (Jun 28, 2023)
8-123077249-T-G		not specified	Uncertain significance (Jan 03, 2024)
8-123082730-G-A		not specified	Uncertain significance (Jan 24, 2023)
8-123082757-C-T		not specified	Uncertain significance (Dec 07, 2022)
8-123084202-A-G		TBC1D31-related disorder	Likely benign (Sep 15, 2020)
8-123084225-A-G		not specified	Uncertain significance (May 24, 2023)
8-123084242-G-A		not specified	Uncertain significance (Aug 02, 2021)
8-123084336-A-G		not specified	Uncertain significance (Jun 17, 2024)
8-123093616-C-T		TBC1D31-related disorder	Likely benign (Apr 11, 2022)
8-123093636-G-T		not specified	Uncertain significance (Jun 07, 2024)
8-123093711-A-T		not specified	Uncertain significance (Jan 19, 2024)
8-123093726-G-A		not specified	Uncertain significance (Aug 30, 2021)
8-123097290-G-A		not specified	Uncertain significance (Feb 27, 2024)
8-123097305-G-C		not specified	Uncertain significance (Jan 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D31	protein_coding	protein_coding	ENST00000287380	22	110186

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.60e-20	0.933	125581	0	166	125747	0.000660

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.906	486	546	0.891	0.0000272	7063
Missense in Polyphen		88	116.91	0.75273		1524
Synonymous	1.14	168	188	0.894	0.00000927	1916
Loss of Function	2.47	40	60.7	0.659	0.00000334	703

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00231	0.00230
Ashkenazi Jewish	0.000596	0.000595
East Asian	0.000437	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000718	0.000703
Middle Eastern	0.000437	0.000435
South Asian	0.000533	0.000523
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0998

Intolerance Scores

• rvis_EVS: 0.1
• rvis_percentile_EVS: 60.76

Haploinsufficiency Scores

• pHI: 0.0844
• hipred: N
• hipred_score: 0.492
• ghis: 0.566

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: H

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d31

Gene ontology

• Cellular component: centrosome