TVP23A

protein-coding

trans-golgi network vesicle protein 23 homolog A

Gene summary

This gene encodes a membrane protein associated with the Golgi apparatus, which plays a crucial role in intracellular vesicular transport. The encoded protein is likely associated with the late (trans) Golgi compartments, which are involved in the delivery of secretory and membrane proteins to the endosome, lysosome or the plasma membrane. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

Previous symbols:

FAM18A

MANE transcript

NM_001079512.4

Inheritance

—

ClinVar variants

U:42B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr16:10,760,919-10,818,794

External References & Databases

Ensembl (ENSG00000166676)

Transcript & Mutation Effects

hg38 • Region Span ~57.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TVP23A variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 40

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001079512.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			40 clinvar	1 clinvar		41
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	42	1	0	43

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001079512.4	RefSeq	NP_001072980.1	7	MANE Select
ENST00000299866.13	Ensembl	ENSP00000299866.8	7	MANE Select
NM_001318873.2	RefSeq	NP_001305802.1	5	Standard
ENST00000456096.6	Ensembl	ENSP00000411972.2	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein secretion
vesicle-mediated transport

Cellular Component

integral component of Golgi membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000299866
Coding exons: 7
Length: 57876
Individuals with no LoFs: 124608
Homozygous LoFs: 1
Heterozygous LoFs: 55
Defined: 124664
p: 0.000225

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.104	108	111	0.972	0.00000556	1388
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00035	0.00032	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00021	0.00020	rare
South Asian	0.00062	0.00056	rare
Other	0.00035	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0635

Intolerance Scores

RVIS EVS: -0.38
RVIS percentile EVS: 27.42

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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