SLC6A7

solute carrier family 6 member 7, the group of Solute carrier family 6

Basic information

Region (hg38): 5:150190061-150222788

Links

ENSG00000011083 ∙ NCBI:6534 ∙ OMIM:606205 ∙ HGNC:11054 ∙ Uniprot:Q99884 ∙ 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 SLC6A7 gene.

• Inborn genetic diseases (35 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC6A7 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					2	2
missense			36			36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	0	2

Variants in SLC6A7

This is a list of pathogenic ClinVar variants found in the SLC6A7 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-150190335-A-G			Uncertain significance (Jul 01, 2017)
5-150194776-G-C		not specified	Uncertain significance (Aug 06, 2021)
5-150194846-T-C		not specified	Uncertain significance (Jan 16, 2024)
5-150194894-C-T		not specified	Uncertain significance (Oct 27, 2023)
5-150197122-C-T		not specified	Uncertain significance (Sep 06, 2022)
5-150197161-T-G		not specified	Uncertain significance (Sep 17, 2021)
5-150197230-C-G		not specified	Uncertain significance (May 27, 2022)
5-150199230-G-A		not specified	Uncertain significance (Jan 29, 2024)
5-150199235-G-A		not specified	Uncertain significance (Aug 08, 2023)
5-150199257-A-C		not specified	Uncertain significance (Aug 16, 2021)
5-150199283-C-T		not specified	Uncertain significance (Dec 18, 2023)
5-150199284-G-A		not specified	Uncertain significance (Mar 21, 2023)
5-150199292-C-T		not specified	Uncertain significance (Oct 26, 2021)
5-150199314-C-T		not specified	Uncertain significance (Oct 20, 2023)
5-150199333-C-T			Benign (Mar 30, 2018)
5-150199346-G-A		not specified	Uncertain significance (Jun 10, 2022)
5-150201184-C-A		not specified	Uncertain significance (Nov 27, 2023)
5-150202393-G-A		not specified	Uncertain significance (Jun 11, 2021)
5-150202596-C-T		not specified	Uncertain significance (Sep 20, 2023)
5-150202646-G-A		not specified	Uncertain significance (Jan 04, 2022)
5-150202676-G-A		not specified	Uncertain significance (Aug 14, 2023)
5-150202680-C-T		not specified	Uncertain significance (May 30, 2023)
5-150203750-A-G		not specified	Uncertain significance (Feb 15, 2023)
5-150203928-G-T		not specified	Uncertain significance (Mar 29, 2022)
5-150203964-C-T		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC6A7	protein_coding	protein_coding	ENST00000230671	14	32832

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.55e-10	0.956	125682	0	66	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.520	360	389	0.926	0.0000233	4106
Missense in Polyphen		159	190.47	0.83479		2080
Synonymous	0.249	164	168	0.976	0.0000109	1309
Loss of Function	2.08	20	32.9	0.608	0.00000162	346

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000235	0.000235
Ashkenazi Jewish	0.000201	0.000198
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000318	0.000316
Middle Eastern	0.000272	0.000272
South Asian	0.000498	0.000490
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Terminates the action of proline by its high affinity sodium-dependent reuptake into presynaptic terminals.
• Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway;Amine compound SLC transporters;Metabolism of polyamines;Metabolism of amino acids and derivatives;Metabolism;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Na+/Cl- dependent neurotransmitter transporters;Creatine metabolism (Consensus)

Recessive Scores

• pRec: 0.513

Intolerance Scores

• loftool: 0.473
• rvis_EVS: -1.29
• rvis_percentile_EVS: 5.08

Haploinsufficiency Scores

• pHI: 0.215
• hipred: Y
• hipred_score: 0.554
• ghis: 0.681

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.240

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc6a7

Gene ontology

• Biological process: neurotransmitter transport;proline transport;proline transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;membrane
• Molecular function: proline:sodium symporter activity;neurotransmitter:sodium symporter activity;L-proline transmembrane transporter activity