GeneBe

SLC17A7

protein-coding

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

Gene summary

The protein encoded by this gene is a vesicle-bound, sodium-dependent phosphate transporter that is specifically expressed in the neuron-rich regions of the brain. It is preferentially associated with the membranes of synaptic vesicles and functions in glutamate transport. The protein shares 82% identity with the differentiation-associated Na-dependent inorganic phosphate cotransporter and they appear to form a distinct class within the Na+/Pi cotransporter family. [provided by RefSeq, Jul 2008]

MANE transcript

NM_020309.4

Inheritance

—

ClinVar variants

U:42B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr19:49,429,401-49,442,360

External References & Databases

Ensembl (ENSG00000104888)NCBI Gene (57030)OMIM (605208)HGNC:16704GenCCUniProt (Q9P2U7)AlphaFoldClinVar (SLC17A7)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~13.0 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC17A7 variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 39
not providedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020309.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
3
clinvar
 4
missense
41
clinvar
1
clinvar
1
clinvar
 43
nonsense
0
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
0
Total00422448
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_020309.4RefSeqNP_064705.112MANE Select
ENST00000221485.8EnsemblENSP00000221485.212MANE Select
ENST00000596689.1EnsemblENSP00000472086.14Standard
ENST00000600601.5EnsemblENSP00000470338.111Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
slc17a7aDanio rerio

Structure: eye

Quality: decreased size

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • 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

Biological Process

  • neural retina development
  • ion transport
  • phosphate ion transport
  • brain development
  • long-term memory

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

Cellular Component

  • plasma membrane
  • integral component of membrane
  • cell junction
  • integral component of synaptic vesicle membrane
  • synaptic vesicle membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000221485
Coding exons
12
Length
12960
Individuals with no LoFs
125742
Homozygous LoFs
0
Heterozygous LoFs
4
Defined
125746
p
0.0000159
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.491783660.4870.00002143631
Missense (PolyPhen)1381.2520.16787
Synonymous0.02711571570.9970.00001041135
Loss of Function4.70025.80.000.00000110285

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian0.0000540.000054rare
Finnish00.0absent
European (Non-Finnish)0.0000180.000018rare
South Asian0.0000330.000033rare
Other00.0absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec
0.250

Intolerance Scores

LoFtool
0.135
RVIS EVS
-0.31
RVIS percentile EVS
31.93

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
S
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.114

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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