TVP23A

trans-golgi network vesicle protein 23 homolog A

Basic information

Region (hg38): 16:10760919-10818794

Previous symbols: [ "FAM18A" ]

Links

ENSG00000166676 ∙ NCBI:780776 ∙ ∙ HGNC:20398 ∙ Uniprot:A6NH52 ∙ 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 TVP23A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TVP23A 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			10	2		12
Total	0	0	25	3	0

Variants in TVP23A

This is a list of pathogenic ClinVar variants found in the TVP23A region.

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

Position	Type	Phenotype	Significance	ClinVar
16-10761447-G-C		not specified	Uncertain significance (Mar 21, 2022)
16-10761448-A-C		not specified	Uncertain significance (Mar 06, 2023)
16-10761772-T-A		not specified	Uncertain significance (Jun 06, 2023)
16-10761791-G-A		not specified	Uncertain significance (Aug 17, 2022)
16-10761792-C-T			Likely benign (Jan 01, 2023)
16-10761793-G-A		not specified	Uncertain significance (Dec 30, 2023)
16-10761811-G-C		not specified	Uncertain significance (Jan 18, 2022)
16-10761820-G-A		not specified	Likely benign (Aug 21, 2023)
16-10761848-A-G		not specified	Uncertain significance (Oct 04, 2022)
16-10767982-T-C		not specified	Uncertain significance (Dec 16, 2022)
16-10767982-T-G		not specified	Uncertain significance (Jan 19, 2024)
16-10768011-G-C		not specified	Uncertain significance (Jun 16, 2024)
16-10769049-A-T		not specified	Uncertain significance (Mar 26, 2024)
16-10769056-A-G		not specified	Uncertain significance (Mar 28, 2023)
16-10770278-C-G		not specified	Uncertain significance (Sep 25, 2023)
16-10770288-T-C		not specified	Uncertain significance (Dec 13, 2023)
16-10770298-C-T		not specified	Likely benign (Nov 05, 2021)
16-10771684-T-A		not specified	Uncertain significance (Nov 02, 2023)
16-10771713-C-T		not specified	Uncertain significance (Jul 19, 2023)
16-10773346-A-T		not specified	Uncertain significance (Aug 12, 2021)
16-10773399-T-C		not specified	Uncertain significance (Dec 13, 2023)
16-10773404-G-T		not specified	Uncertain significance (May 11, 2022)
16-10773412-T-G		not specified	Uncertain significance (May 17, 2023)
16-10774052-A-C		not specified	Uncertain significance (Jun 22, 2023)
16-10774080-C-T		not specified	Uncertain significance (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TVP23A	protein_coding	protein_coding	ENST00000299866	7	57876

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.69e-7	0.421	124608	1	55	124664	0.000225

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.104	108	111	0.972	0.00000556	1388
Missense in Polyphen		36	45.906	0.78421		594
Synonymous	0.0818	44	44.7	0.984	0.00000257	392
Loss of Function	0.735	12	15.1	0.796	8.95e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000525	0.000499
Ashkenazi Jewish	0.000104	0.0000994
East Asian	0.000115	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000209	0.000203
Middle Eastern	0.000115	0.000111
South Asian	0.000620	0.000556
Other	0.000347	0.000330

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0635

Intolerance Scores

• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• pHI: 0.117
• hipred: N
• hipred_score: 0.216
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tvp23a

Gene ontology

• Biological process: protein secretion;vesicle-mediated transport
• Cellular component: integral component of Golgi membrane