SLC18A1

solute carrier family 18 member A1, the group of Solute carrier family 18

Basic information

Region (hg38): 8:20144854-20183206

Previous symbols: [ "VMAT1", "VAT1" ]

Links

ENSG00000036565 ∙ NCBI:6570 ∙ OMIM:193002 ∙ HGNC:10934 ∙ Uniprot:P54219 ∙ 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 SLC18A1 gene.

• Inborn genetic diseases (35 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC18A1 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			33	2		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	2	0

Variants in SLC18A1

This is a list of pathogenic ClinVar variants found in the SLC18A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-20145782-T-C		not specified	Uncertain significance (Mar 29, 2022)
8-20145845-G-T		not specified	Uncertain significance (Feb 23, 2023)
8-20145870-G-A		not specified	Likely benign (Dec 12, 2023)
8-20147277-G-A		not specified	Uncertain significance (May 18, 2023)
8-20147283-C-T		not specified	Uncertain significance (Oct 14, 2023)
8-20147310-T-C		not specified	Uncertain significance (Feb 28, 2023)
8-20147317-T-A		not specified	Uncertain significance (Jan 22, 2024)
8-20147355-C-A		not specified	Uncertain significance (May 23, 2023)
8-20147367-A-C		not specified	Uncertain significance (Dec 14, 2021)
8-20147377-C-A		not specified	Uncertain significance (Mar 04, 2024)
8-20147636-C-T		not specified	Uncertain significance (Nov 03, 2023)
8-20147639-T-C		not specified	Uncertain significance (Oct 20, 2021)
8-20147672-G-A		not specified	Uncertain significance (Jul 06, 2021)
8-20147699-G-T		not specified	Uncertain significance (Feb 13, 2024)
8-20148022-G-C		not specified	Uncertain significance (Mar 02, 2023)
8-20148049-A-G		not specified	Uncertain significance (Aug 15, 2023)
8-20150667-G-A		not specified	Uncertain significance (Aug 09, 2021)
8-20150681-G-C		not specified	Uncertain significance (Sep 07, 2022)
8-20164872-G-C		not specified	Uncertain significance (Apr 20, 2023)
8-20164884-G-T		not specified	Uncertain significance (Jun 22, 2021)
8-20164961-G-A		not specified	Uncertain significance (Apr 10, 2023)
8-20165098-C-T		not specified	Uncertain significance (Jul 27, 2022)
8-20171120-A-T		not specified	Uncertain significance (Sep 12, 2023)
8-20171122-G-T		not specified	Uncertain significance (Jun 29, 2023)
8-20171129-G-C		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC18A1	protein_coding	protein_coding	ENST00000440926	15	38352

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.80e-21	0.000276	125534	0	214	125748	0.000851

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.38	420	303	1.39	0.0000161	3382
Missense in Polyphen		191	128.78	1.4832		1479
Synonymous	-2.08	143	115	1.25	0.00000632	1079
Loss of Function	-0.783	29	24.8	1.17	0.00000124	279

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00418	0.00417
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000935	0.000925
Finnish	0.00	0.00
European (Non-Finnish)	0.000294	0.000290
Middle Eastern	0.000935	0.000925
South Asian	0.000909	0.000882
Other	0.000842	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the transport of biogenic monoamines, such as serotonin, from the cytoplasm into the secretory vesicles of neuroendocrine and endocrine cells. {ECO:0000269|PubMed:16326835, ECO:0000269|PubMed:8643547}.
• Pathway: Synaptic vesicle cycle - Homo sapiens (human);Serotonergic synapse - Homo sapiens (human);Dopaminergic synapse - Homo sapiens (human);Amphetamine addiction - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);Alcoholism - Homo sapiens (human);Cocaine addiction - Homo sapiens (human);Sympathetic Nerve Pathway (Neuroeffector Junction);Synaptic Vesicle Pathway;Amine compound SLC transporters;Tyrosine metabolism;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Histidine metabolism;Tryptophan metabolism;Na+/Cl- dependent neurotransmitter transporters (Consensus)

Recessive Scores

• pRec: 0.205

Intolerance Scores

• loftool: 0.609
• rvis_EVS: 1.03
• rvis_percentile_EVS: 91.09

Haploinsufficiency Scores

• pHI: 0.0910
• hipred: N
• hipred_score: 0.275

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.634

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc18a1
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype

Gene ontology

• Biological process: neurotransmitter transport;drug transmembrane transport;aminergic neurotransmitter loading into synaptic vesicle;monoamine transport;serotonin uptake
• Cellular component: endoplasmic reticulum membrane;integral component of membrane;cell junction;synaptic vesicle membrane;terminal bouton;clathrin-sculpted monoamine transport vesicle membrane
• Molecular function: serotonin:sodium symporter activity;monoamine transmembrane transporter activity;drug transmembrane transporter activity