TVP23B

trans-golgi network vesicle protein 23 homolog B

Basic information

Region (hg38): 17:18781111-18806714

Previous symbols: [ "FAM18B", "FAM18B1" ]

Links

ENSG00000171928 ∙ NCBI:51030 ∙ ∙ HGNC:20399 ∙ Uniprot:Q9NYZ1 ∙ 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 TVP23B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TVP23B 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	11	0	0

Variants in TVP23B

This is a list of pathogenic ClinVar variants found in the TVP23B region.

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

Position	Type	Phenotype	Significance	ClinVar
17-18789374-G-A		not specified	Uncertain significance (Jan 22, 2024)
17-18789405-C-T		not specified	Uncertain significance (Jul 14, 2023)
17-18790924-T-C		not specified	Uncertain significance (Sep 15, 2021)
17-18798882-G-A		not specified	Uncertain significance (Feb 02, 2024)
17-18798884-C-T		not specified	Uncertain significance (Jul 26, 2022)
17-18798914-G-A		not specified	Uncertain significance (Apr 25, 2022)
17-18798918-T-C		not specified	Uncertain significance (Jul 12, 2022)
17-18804138-G-T		not specified	Uncertain significance (Sep 22, 2022)
17-18804169-G-T		not specified	Uncertain significance (Feb 07, 2023)
17-18804225-A-G		not specified	Uncertain significance (Sep 19, 2022)
17-18805548-G-C		not specified	Uncertain significance (Feb 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TVP23B	protein_coding	protein_coding	ENST00000307767	7	25720

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000517	0.894	125663	0	80	125743	0.000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.673	90	110	0.819	0.00000557	1349
Missense in Polyphen		12	21.251	0.56469		299
Synonymous	-0.108	40	39.1	1.02	0.00000210	370
Loss of Function	1.44	7	12.5	0.561	5.94e-7	146

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000248	0.000244
Ashkenazi Jewish	0.00326	0.00318
East Asian	0.0000585	0.0000544
Finnish	0.000659	0.000647
European (Non-Finnish)	0.000171	0.000167
Middle Eastern	0.0000585	0.0000544
South Asian	0.000133	0.000131
Other	0.000538	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.100

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.351
• hipred: N
• hipred_score: 0.496
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tvp23b

Gene ontology

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