SLC46A2

protein-coding

solute carrier family 46 member 2, the group of Solute carrier family 46

Gene summary

Enables cyclic-GMP-AMP transmembrane transporter activity. Involved in cyclic-GMP-AMP transmembrane import across plasma membrane and positive regulation of nucleotide-binding activity oligomerization domain containing 1 signaling pathway. Located in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

TSCOT

MANE transcript

NM_033051.4

Inheritance

—

ClinVar variants

U:87B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.08

Max pathogenic AF

—

Genomic locus

chr9:112,878,920-112,890,876

External References & Databases

Ensembl (ENSG00000119457)

Transcript & Mutation Effects

hg38 • Region Span ~12.0 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 SLC46A2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 90

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033051.4. 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					3 clinvar	3
missense			87 clinvar	4 clinvar	1 clinvar	92
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	87	4	4	95

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033051.4	RefSeq	NP_149040.3	4	MANE Select
ENST00000374228.5	Ensembl	ENSP00000363345.4	4	MANE Select
ENST00000491462.2	Ensembl	ENSP00000474847.1	2	Standard
ENST00000868988.1	Ensembl	ENSP00000539047.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

T cell homeostasis
regulation of T cell differentiation
thymus development
transmembrane transport
negative regulation of T cell apoptotic process

Molecular Function

symporter activity

Cellular Component

plasma membrane
cell surface
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374228
Coding exons: 4
Length: 11994
Individuals with no LoFs: 125647
Homozygous LoFs: 0
Heterozygous LoFs: 101
Defined: 125748
p: 0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.147	285	292	0.976	0.0000164	3011
Missense (PolyPhen)		112	126.32	0.88661		1349
Synonymous	1.08	120	136	0.882	0.00000840	1076
Loss of Function	-0.297	16	14.8	1.08	7.44e-7	152

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00044	0.00043	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00098	0.00098	rare
Finnish	0.00032	0.00032	rare
European (Non-Finnish)	0.00027	0.00027	rare
South Asian	0.00069	0.00069	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as a transporter. {ECO:0000250}.;

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.468
RVIS EVS: 0.53
RVIS percentile EVS: 80.96

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.168

Gene Damage Prediction

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