SLC35F1

protein-coding

solute carrier family 35 member F1, the group of Solute carrier family 35

Gene summary

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]

Previous symbols:

C6orf169

MANE transcript

NM_001029858.4

Inheritance

ClinVar variants

U:48B:1

Top phenotype

Neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.13

Max pathogenic AF

—

Genomic locus

chr6:117,907,264-118,317,676

External References & Databases

Ensembl (ENSG00000196376)

Transcript & Mutation Effects

hg38 • Region Span ~410.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC35F1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 41

not providedTotal: 2

Neurodevelopmental disorderTotal: 1

Nephrotic syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001029858.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			46 clinvar			46
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	48	0	1	49

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001029858.4	RefSeq	NP_001025029.2	8	MANE Select
ENST00000360388.9	Ensembl	ENSP00000353557.4	8	MANE Select
NM_001415931.1	RefSeq	NP_001402860.1	8	Standard
ENST00000621341.1	Ensembl	ENSP00000484738.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

transmembrane transport

Molecular Function

transmembrane transporter activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000360388
Coding exons: 8
Length: 410151
Individuals with no LoFs: 125741
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125748
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.78	144	218	0.661	0.0000111	2591
Missense (PolyPhen)		20	53.74	0.37216		701
Synonymous	1.01	77	89.1	0.864	0.00000464	854
Loss of Function	3.83	3	22.7	0.132	0.00000142	236

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Putative solute transporter. {ECO:0000305}.;

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.266
RVIS EVS: 0.06
RVIS percentile EVS: 58.53

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.307

Gene Damage Prediction

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