SLC5A7

Chr 2

solute carrier family 5 member 7

Also known as: CHT, CHT1, CMS20, DHMNVP, HMN7A, HMND7, hCHT1

NCBI Gene: 60482ENSG00000115665UniProt: Q9GZV3

This gene encodes a sodium ion- and chloride ion-dependent high-affinity transporter that mediates choline uptake for acetylcholine synthesis in cholinergic neurons. The protein transports choline from the extracellular space into presynaptic terminals for synthesis into acetylcholine. Increased choline uptake results from increased density of this protein in synaptosomal plasma membranes in response to depolarization of cholinergic terminals. Dysfunction of cholinergic signaling has been implicated in various disorders including depression, attention-deficit disorder, and schizophrenia. An allelic variant of this gene is associated with autosomal dominant distal hereditary motor neuronopathy type VIIA. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtNeuronopathy, distal hereditary motor, autosomal dominant 7
UniProtMyasthenic syndrome, congenital, 20, presynaptic

Clinical highlights

Gene-disease validity (ClinGen)
neuronopathy, distal hereditary motor, type 7A · ADModerateconsider for supplementary testing
Interpreting a novel variant
This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Curated gene-level mechanism — a prior for triage, not a per-variant call.
0
Active trials
11
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.56
LOEUF
Multiple*
Mechanism· predicted
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GeneReview available — SLC5A7
Authoritative clinical overview · Recommended first read
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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?
0.56LOEUF
pLI 0.015
Z-score 3.23
OE 0.31 (0.18–0.56)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?
2.81Z-score
OE missense 0.56 (0.49–0.63)
180 obs / 321.6 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?
LoF OE?0.31 (0.18–0.56)
0≤0.351.4
Missense OE?0.56 (0.49–0.63)
0≤0.61.4
Synonymous OE?1.02
0≤1.21.6
LoF obs/exp: 8 / 25.7Missense obs/exp: 180 / 321.6Syn Z: -0.14

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

SLC5A7 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients