SLC35F5

protein-coding

solute carrier family 35 member F5, the group of MicroRNA protein coding host genes|Solute carrier family 35

Gene summary

Enables choline transmembrane transporter activity. Involved in choline transport. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_025181.5

Inheritance

ClinVar variants

U:67B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.55

Max pathogenic AF

—

Genomic locus

chr2:113,705,011-113,756,693

External References & Databases

Ensembl (ENSG00000115084)

Transcript & Mutation Effects

hg38 • Region Span ~51.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

multiple congenital anomalies/dysmorphic syndromeLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0019042

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC35F5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 63

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_025181.5. 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			2 clinvar			2
missense			61 clinvar	3 clinvar		64
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	67	3	0	70

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 58 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_025181.5	RefSeq	NP_079457.2	15	MANE Select
ENST00000245680.7	Ensembl	ENSP00000245680.2	15	MANE Select
NM_001330314.2	RefSeq	NP_001317243.1	15	Standard
NM_001330315.2	RefSeq	NP_001317244.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000245680
Coding exons: 15
Length: 51813
Individuals with no LoFs: 125704
Homozygous LoFs: 0
Heterozygous LoFs: 42
Defined: 125746
p: 0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.979	230	276	0.834	0.0000133	3417
Missense (PolyPhen)		28	54.762	0.5113		695
Synonymous	-0.174	93	90.9	1.02	0.00000445	1003
Loss of Function	2.28	17	30.6	0.555	0.00000153	358

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00013	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00021	0.00021	rare
South Asian	0.00024	0.00023	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0998

Intolerance Scores

RVIS EVS: 0.06
RVIS percentile EVS: 58.74

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.595

Gene Damage Prediction

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