SLC36A3

protein-coding

solute carrier family 36 member 3, the group of Solute carrier family 36

Gene summary

Predicted to enable amino acid transmembrane transporter activity. Predicted to be involved in carboxylic acid transport and proton transmembrane transport. Predicted to be located in membrane. Predicted to be active in vacuolar membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_181774.4

Inheritance

—

ClinVar variants

U:75B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr5:151,276,358-151,303,766

External References & Databases

Ensembl (ENSG00000186334)

Transcript & Mutation Effects

hg38 • Region Span ~27.4 kb

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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 SLC36A3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 76

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_181774.4. 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			74 clinvar	2 clinvar		76
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	75	2	0	77

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_181774.4	RefSeq	NP_861439.3	10	MANE Select
ENST00000335230.8	Ensembl	ENSP00000334750.3	10	MANE Select
NM_001145017.2	RefSeq	NP_001138489.1	11	Standard
ENST00000377713.3	Ensembl	ENSP00000366942.3	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

amino acid transmembrane transport
L-alanine transport
glycine transport
proline transmembrane transport
proton transmembrane transport

Molecular Function

amino acid:proton symporter activity
proton transmembrane transporter activity
amino acid transmembrane transporter activity
L-alanine transmembrane transporter activity
glycine transmembrane transporter activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000377713
Coding exons: 11
Length: 27005
Individuals with no LoFs: 125698
Homozygous LoFs: 0
Heterozygous LoFs: 50
Defined: 125748
p: 0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0858	264	260	1.01	0.0000134	3319
Missense (PolyPhen)		51	55.675	0.91603		702
Synonymous	0.809	97	108	0.901	0.00000617	1022
Loss of Function	2.52	8	20.3	0.395	9.53e-7	280

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0011	0.0011	notable
Latino/Admixed American	0.00047	0.00046	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000063	0.000062	rare
South Asian	0.000098	0.000098	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0998

Intolerance Scores

LoFtool: 0.937
RVIS EVS: 0.29
RVIS percentile EVS: 71.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.147

Gene Damage Prediction

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