SLC2A4RG

protein-coding

SLC2A4 regulator

Gene summary

The protein encoded by this gene is a nuclear transcription factor involved in the activation of the solute carrier family 2 member 4 gene. The encoded protein interacts with another transcription factor, myocyte enhancer factor 2, to activate transcription of this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_020062.4

Inheritance

—

ClinVar variants

U:81B:10

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.26

Max pathogenic AF

—

Genomic locus

chr20:63,739,776-63,744,050

External References & Databases

Ensembl (ENSG00000125520)

Transcript & Mutation Effects

hg38 • Region Span ~4.3 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 SLC2A4RG variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 80

not providedTotal: 4

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020062.4. 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			2 clinvar	1 clinvar	1 clinvar	4
missense			77 clinvar	7 clinvar	1 clinvar	85
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	81	8	2	91

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020062.4	RefSeq	NP_064446.2	8	MANE Select
ENST00000266077.5	Ensembl	ENSP00000266077.2	8	MANE Select
ENST00000872204.1	Ensembl	ENSP00000542263.1	8	Standard
ENST00000872204.2	Ensembl	ENSP00000542263.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

AMP-activated Protein Kinase (AMPK) Signaling

Biological Process

regulation of transcription, DNA-templated

Molecular Function

DNA binding
DNA-binding transcription factor activity
metal ion binding

Cellular Component

nucleus
cytoplasm
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000266077
Coding exons: 8
Length: 3645
Individuals with no LoFs: 125066
Homozygous LoFs: 1
Heterozygous LoFs: 140
Defined: 125207
p: 0.000563

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.188	181	188	0.961	0.0000123	2413
Missense (PolyPhen)		55	76.334	0.72051		812
Synonymous	-0.564	93	86.3	1.08	0.00000603	874
Loss of Function	2.31	3	11.4	0.263	4.85e-7	171

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00023	0.00019	rare
Latino/Admixed American	0.00090	0.00081	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00013	0.00011	rare
Finnish	0.00016	0.00014	rare
European (Non-Finnish)	0.00039	0.00033	rare
South Asian	0.0023	0.0021	notable
Other	0.00089	0.00082	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcription factor involved in SLC2A4 and HD gene transactivation. Binds to the consensus sequence 5'-GCCGGCG-3'. {ECO:0000269|PubMed:14625278, ECO:0000269|PubMed:14630949}.;

Recessive Scores

pRec: 0.213

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.977

Gene Damage Prediction

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