VAT1L

vesicle amine transport 1 like

Basic information

Region (hg38): 16:77788563-77980107

Links

ENSG00000171724 ∙ NCBI:57687 ∙ OMIM:620202 ∙ HGNC:29315 ∙ Uniprot:Q9HCJ6 ∙ 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 VAT1L gene.

• Inborn genetic diseases (21 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VAT1L 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in VAT1L

This is a list of pathogenic ClinVar variants found in the VAT1L region.

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

Position	Type	Phenotype	Significance	ClinVar
16-77788698-G-A		not specified	Uncertain significance (Oct 30, 2023)
16-77788708-C-A		not specified	Uncertain significance (Jun 13, 2022)
16-77788726-T-A		not specified	Uncertain significance (Feb 05, 2024)
16-77788776-G-A		not specified	Uncertain significance (Jan 23, 2024)
16-77788777-G-C		not specified	Uncertain significance (May 17, 2023)
16-77788788-C-T		not specified	Uncertain significance (Feb 23, 2023)
16-77788797-G-A		not specified	Uncertain significance (Apr 07, 2022)
16-77788798-C-T		not specified	Uncertain significance (Apr 04, 2023)
16-77816980-C-G		not specified	Uncertain significance (Jul 14, 2021)
16-77825351-G-A		not specified	Uncertain significance (Jan 30, 2024)
16-77825381-A-G		not specified	Uncertain significance (Oct 26, 2022)
16-77825417-C-T		not specified	Uncertain significance (Apr 07, 2023)
16-77862778-G-T		not specified	Uncertain significance (Oct 12, 2022)
16-77862806-C-G		not specified	Uncertain significance (Mar 08, 2024)
16-77862853-T-G		not specified	Uncertain significance (Mar 31, 2022)
16-77862874-G-T		not specified	Uncertain significance (Oct 29, 2021)
16-77876374-T-C		not specified	Uncertain significance (Dec 08, 2023)
16-77876396-T-A		not specified	Uncertain significance (May 15, 2023)
16-77876450-C-G		not specified	Uncertain significance (Mar 21, 2022)
16-77879175-C-G		not specified	Uncertain significance (Feb 05, 2024)
16-77879180-A-G		not specified	Uncertain significance (Oct 13, 2023)
16-77879203-C-G		not specified	Uncertain significance (Aug 12, 2022)
16-77884719-C-T		not specified	Uncertain significance (Jun 28, 2023)
16-77884737-C-A		not specified	Uncertain significance (Dec 28, 2022)
16-77884741-T-C		not specified	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VAT1L	protein_coding	protein_coding	ENST00000302536	9	191578

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.94e-7	0.790	125725	0	22	125747	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.754	264	232	1.14	0.0000122	2720
Missense in Polyphen		77	85.585	0.89969		1020
Synonymous	-1.57	107	88.3	1.21	0.00000483	797
Loss of Function	1.34	12	18.1	0.662	8.55e-7	236

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.00	0.00
South Asian	0.0000713	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.681
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.34

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.575
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.252

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vat1l
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: oxidation-reduction process
• Molecular function: protein binding;zinc ion binding;oxidoreductase activity