SLC17A7

solute carrier family 17 member 7, the group of Solute carrier family 17

Basic information

Region (hg38): 19:49429400-49442360

Links

ENSG00000104888 ∙ NCBI:57030 ∙ OMIM:605208 ∙ HGNC:16704 ∙ Uniprot:Q9P2U7 ∙ 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 SLC17A7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC17A7 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	3	4
missense			16	1	1	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	16	2	5

Variants in SLC17A7

This is a list of pathogenic ClinVar variants found in the SLC17A7 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-49430529-C-T			Likely benign (Jan 01, 2023)
19-49430542-G-A		not specified	Uncertain significance (Oct 12, 2022)
19-49430554-G-A			Uncertain significance (Dec 01, 2016)
19-49430575-C-T		not specified	Uncertain significance (Oct 29, 2021)
19-49430591-G-T			Benign (Apr 06, 2018)
19-49430598-G-C		not specified	Uncertain significance (Sep 26, 2022)
19-49430611-G-A		not specified	Uncertain significance (Mar 16, 2022)
19-49430638-T-C		not specified	Uncertain significance (Jun 07, 2024)
19-49430668-C-T		not specified	Uncertain significance (Jul 19, 2022)
19-49430689-C-T		not specified	Uncertain significance (Jan 23, 2024)
19-49430690-G-A			Benign (Jun 13, 2018)
19-49430725-C-T		not specified	Uncertain significance (Jan 10, 2022)
19-49431395-C-T		not specified	Uncertain significance (Nov 30, 2022)
19-49431439-A-G		not specified	Uncertain significance (Oct 26, 2021)
19-49432602-G-T		not specified	Uncertain significance (Jan 09, 2024)
19-49432916-G-C			Likely benign (Apr 01, 2023)
19-49433716-G-T			Benign (Jun 13, 2018)
19-49433817-G-C		not specified	Uncertain significance (Nov 21, 2022)
19-49433830-C-T		not specified	Uncertain significance (Aug 26, 2022)
19-49433865-C-T		not specified	Uncertain significance (Sep 01, 2021)
19-49434053-G-A			Benign (Apr 06, 2018)
19-49434613-G-A		not specified	Uncertain significance (Mar 29, 2023)
19-49434679-T-G		not specified	Uncertain significance (Apr 01, 2024)
19-49435203-T-C			Benign (Mar 29, 2018)
19-49436665-T-C		not specified	Uncertain significance (Oct 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC17A7	protein_coding	protein_coding	ENST00000221485	12	12960

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000117	125742	0	4	125746	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.49	178	366	0.487	0.0000214	3631
Missense in Polyphen		13	81.252	0.16		787
Synonymous	0.0271	157	157	0.997	0.0000104	1135
Loss of Function	4.70	0	25.8	0.00	0.00000110	285

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates the uptake of glutamate into synaptic vesicles at presynaptic nerve terminals of excitatory neural cells. May also mediate the transport of inorganic phosphate. {ECO:0000269|PubMed:10820226}.
• Pathway: Synaptic vesicle cycle - Homo sapiens (human);Retrograde endocannabinoid signaling - Homo sapiens (human);Glutamatergic synapse - Homo sapiens (human);Nicotine addiction - Homo sapiens (human);Synaptic Vesicle Pathway;Organic anion transporters;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)

Recessive Scores

• pRec: 0.250

Intolerance Scores

• loftool: 0.135
• rvis_EVS: -0.31
• rvis_percentile_EVS: 31.93

Haploinsufficiency Scores

• pHI: 0.227
• hipred: Y
• hipred_score: 0.799
• ghis: 0.585

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc17a7
• Phenotype: growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); vision/eye 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)

Zebrafish Information Network

• Gene name: slc17a7a
• Affected structure: eye
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: neural retina development;ion transport;phosphate ion transport;brain development;long-term memory;glutamate secretion;L-glutamate transmembrane transport;synaptic transmission, glutamatergic;sodium ion transmembrane transport;sequestering of neurotransmitter;sodium-dependent phosphate transport;regulation of synapse structure or activity;L-glutamate import;excitatory postsynaptic potential;synaptic vesicle lumen acidification;neurotransmitter loading into synaptic vesicle;regulation of synaptic vesicle endocytosis;chloride transmembrane transport
• Cellular component: plasma membrane;integral component of membrane;cell junction;integral component of synaptic vesicle membrane;synaptic vesicle membrane;cerebellar mossy fiber;presynaptic active zone;excitatory synapse;clathrin-sculpted glutamate transport vesicle membrane;postsynapse
• Molecular function: L-glutamate transmembrane transporter activity;neurotransmitter transporter activity;extracellularly glutamate-gated chloride channel activity;sodium:inorganic phosphate symporter activity;sodium-dependent phosphate transmembrane transporter activity