TBC1D29P

TBC1 domain family member 29, pseudogene

Basic information

Region (hg38): 17:30553502-30562917

Previous symbols: [ "TBC1D29" ]

Links

ENSG00000266733 ∙ NCBI:26083 ∙ ∙ HGNC:24509 ∙ Uniprot:Q9UFV1 ∙ 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 TBC1D29P gene.

• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D29P 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding			1			1
Total	0	0	2	0	0

Variants in TBC1D29P

This is a list of pathogenic ClinVar variants found in the TBC1D29P region.

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

Position	Type	Phenotype	Significance	ClinVar
17-30560127-G-T		not specified	Uncertain significance (Feb 28, 2024)
17-30560130-T-A		not specified	Uncertain significance (Nov 06, 2023)
17-30560154-G-C		not specified	Uncertain significance (Aug 22, 2023)
17-30560166-G-T		not specified	Uncertain significance (Apr 07, 2022)
17-30560617-A-G		not specified	Uncertain significance (Feb 06, 2023)
17-30560633-C-T		not specified	Uncertain significance (Apr 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D29P	protein_coding	protein_coding	ENST00000580161	5	6382

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000679	0.524	113534	426	11785	125745	0.0498

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0792	81	83.0	0.976	0.00000423	943
Missense in Polyphen		27	32.243	0.83739		382
Synonymous	1.65	20	31.8	0.628	0.00000161	310
Loss of Function	0.315	5	5.82	0.859	2.47e-7	66

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0329	0.0326
Ashkenazi Jewish	0.0339	0.0337
East Asian	0.000382	0.000381
Finnish	0.114	0.113
European (Non-Finnish)	0.0681	0.0672
Middle Eastern	0.000382	0.000381
South Asian	0.0329	0.0318
Other	0.0585	0.0577

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.22
• rvis_percentile_EVS: 67.92

Haploinsufficiency Scores

• pHI: 0.0742
• hipred: N
• hipred_score: 0.123
• ghis: 0.438

Essentials

• essential_gene_gene_trap: N