SLC35F1

Chr 6

solute carrier family 35 member F1

Also known as: C6orf169, dJ230I3.1

NCBI Gene: 222553ENSG00000196376UniProt: Q5T1Q4

Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Located in synaptic vesicle membrane. [provided by Alliance of Genome Resources, Jul 2025]

87
ClinVar variants
28
Pathogenic / LP
0.95
pLI score· haploinsufficient
0
Active trials
Clinical Summary— SLC35F1
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.95). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
28 Pathogenic / Likely Pathogenic· 58 VUS of 87 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.34LOEUF
pLI 0.951
Z-score 3.83
OE 0.13 (0.06–0.34)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.78Z-score
OE missense 0.66 (0.58–0.76)
144 obs / 217.8 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.13 (0.06–0.34)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.66 (0.58–0.76)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.86
0≤1.21.6
LoF obs/exp: 3 / 22.7Missense obs/exp: 144 / 217.8Syn Z: 1.01

ClinVar Variant Classifications

87 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic22
Likely Pathogenic6
VUS58
Benign1
22
Pathogenic
6
Likely Pathogenic
58
VUS
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
22
0
22
Likely Pathogenic
0
0
6
0
6
VUS
0
44
14
0
58
Likely Benign
0
0
0
0
0
Benign
0
0
0
1
1
Total04442187

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

SLC35F1 · protein map & ClinVar variants

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

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Morphological and behavioral analysis of Slc35f1-deficient mice revealed no neurodevelopmental phenotype.
Ehlers JS et al.·Brain Struct Funct
2023
6q22.1 microdeletion and susceptibility to pediatric epilepsy.
Szafranski P et al.·Eur J Hum Genet
2015Case report
Genome-wide association analysis identifies multiple loci related to resting heart rate.
Eijgelsheim M et al.·Hum Mol Genet
2010
Aberrantly Methylated and Expressed Genes as Prognostic Epigenetic Biomarkers for Colon Cancer.
Wu Y et al.·DNA Cell Biol
2020
Tissue-specific mRNA expression profiles of human solute carrier 35 transporters.
Nishimura M et al.·Drug Metab Pharmacokinet
2009
Fine mapping of QT interval regions in global populations refines previously identified QT interval loci and identifies signals unique to African and Hispanic descent populations.
Avery CL et al.·Heart Rhythm
2017
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

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