SLC1A6

solute carrier family 1 member 6, the group of Solute carrier family 1

Basic information

Region (hg38): 19:14950033-15022990

Links

ENSG00000105143 ∙ NCBI:6511 ∙ OMIM:600637 ∙ HGNC:10944 ∙ Uniprot:P48664 ∙ 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 SLC1A6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC1A6 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				1		1
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	1	0

Variants in SLC1A6

This is a list of pathogenic ClinVar variants found in the SLC1A6 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-14950209-C-T		not specified	Uncertain significance (Jul 20, 2022)
19-14950220-C-T		not specified	Uncertain significance (Jul 09, 2021)
19-14950350-T-C		not specified	Uncertain significance (Nov 09, 2021)
19-14950365-C-T		not specified	Uncertain significance (Sep 26, 2023)
19-14952941-C-T		not specified	Uncertain significance (Mar 14, 2023)
19-14953015-G-A		not specified	Uncertain significance (Mar 23, 2022)
19-14956488-C-G		not specified	Uncertain significance (Apr 10, 2023)
19-14956495-C-T		not specified	Uncertain significance (Dec 06, 2021)
19-14956582-C-T		not specified	Uncertain significance (Dec 17, 2023)
19-14956609-C-T		not specified	Uncertain significance (Apr 25, 2023)
19-14956678-C-A		not specified	Uncertain significance (Dec 03, 2021)
19-14962086-C-A		not specified	Uncertain significance (Mar 22, 2023)
19-14962288-C-T		not specified	Uncertain significance (Mar 01, 2023)
19-14962310-C-G		not specified	Uncertain significance (Jan 24, 2024)
19-14968416-G-A		not specified	Likely benign (Mar 07, 2024)
19-14968418-T-C		not specified	Uncertain significance (Dec 19, 2023)
19-14968505-T-C		not specified	Uncertain significance (Jul 28, 2021)
19-14971850-C-T		not specified	Uncertain significance (Aug 02, 2023)
19-14972759-C-T		not specified	Uncertain significance (Feb 12, 2024)
19-14972770-C-A		not specified	Uncertain significance (Dec 01, 2022)
19-14972804-C-T		not specified	Uncertain significance (Mar 31, 2024)
19-14972825-C-A		not specified	Uncertain significance (Jun 30, 2022)
19-15010996-C-G		not specified	Uncertain significance (Dec 18, 2023)
19-15011028-T-A		not specified	Uncertain significance (Sep 13, 2023)
19-15011072-A-G		not specified	Uncertain significance (Apr 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC1A6	protein_coding	protein_coding	ENST00000221742	9	72957

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.762	0.238	125479	0	3	125482	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.67	229	374	0.612	0.0000242	3635
Missense in Polyphen		91	173.22	0.52533		1633
Synonymous	1.02	140	156	0.896	0.0000105	1236
Loss of Function	3.26	3	17.9	0.168	8.48e-7	198

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000180	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sodium-dependent, high-affinity amino acid transporter that mediates the uptake of L-glutamate and also L-aspartate and D-aspartate (PubMed:7791878). Functions as a symporter that transports one amino acid molecule together with two or three Na(+) ions and one proton, in parallel with the counter-transport of one K(+) ion. Mediates Cl(-) flux that is not coupled to amino acid transport; this avoids the accumulation of negative charges due to aspartate and Na(+) symport (By similarity). Plays a redundant role in the rapid removal of released glutamate from the synaptic cleft, which is essential for terminating the postsynaptic action of glutamate (Probable). {ECO:0000250|UniProtKB:O35921, ECO:0000269|PubMed:7791878, ECO:0000305}.
• Pathway: Glutamatergic synapse - Homo sapiens (human);Purine metabolism;Amino acid and oligopeptide SLC transporters;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Neuronal System;Histidine metabolism;Glutamate Neurotransmitter Release Cycle;Neurotransmitter release cycle;Transmission across Chemical Synapses (Consensus)

Intolerance Scores

• loftool: 0.200
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.33

Haploinsufficiency Scores

• pHI: 0.261
• hipred: Y
• hipred_score: 0.809
• ghis: 0.625

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.759

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc1a6
• 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)

Gene ontology

• Biological process: neurotransmitter uptake;ion transport;chemical synaptic transmission;glutamate secretion;aspartate transmembrane transport;L-glutamate transmembrane transport;regulation of membrane potential;L-aspartate transmembrane transport;L-glutamate import across plasma membrane
• Cellular component: Golgi apparatus;plasma membrane;integral component of plasma membrane;membrane;intermediate filament cytoskeleton;glutamatergic synapse;integral component of presynaptic membrane
• Molecular function: high-affinity glutamate transmembrane transporter activity;amino acid transmembrane transporter activity;L-aspartate transmembrane transporter activity;metal ion binding