SLC2A4RG

SLC2A4 regulator

Basic information

Region (hg38): 20:63739775-63744050

Links

ENSG00000125520 ∙ NCBI:56731 ∙ OMIM:609493 ∙ HGNC:15930 ∙ Uniprot:Q9NR83 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC2A4RG gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC2A4RG gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			34	5	1	40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	6	2

Variants in SLC2A4RG

This is a list of pathogenic ClinVar variants found in the SLC2A4RG region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
20-63739976-T-A		not specified	Uncertain significance (Apr 11, 2023)
20-63740028-C-A		not specified	Uncertain significance (Dec 19, 2023)
20-63740383-T-A		not specified	Uncertain significance (Sep 26, 2023)
20-63740384-C-A		not specified	Uncertain significance (Sep 26, 2023)
20-63740459-C-T		not specified	Uncertain significance (Jun 17, 2024)
20-63740473-A-C		not specified	Uncertain significance (Aug 16, 2021)
20-63740495-G-C		not specified	Likely benign (Feb 02, 2022)
20-63740497-A-C		not specified	Uncertain significance (Nov 05, 2021)
20-63740518-G-A		not specified	Uncertain significance (Aug 15, 2023)
20-63741375-C-A		not specified	Uncertain significance (Jan 23, 2024)
20-63741380-G-A		not specified	Uncertain significance (Aug 30, 2021)
20-63741413-G-A		not specified	Uncertain significance (Dec 13, 2021)
20-63741455-G-A		not specified	Uncertain significance (Mar 26, 2024)
20-63741456-C-A		not specified	Uncertain significance (Dec 08, 2023)
20-63741456-C-T		not specified	Uncertain significance (Apr 01, 2024)
20-63741477-C-T		not specified	Uncertain significance (Jan 03, 2022)
20-63741883-C-T		not specified	Uncertain significance (Nov 07, 2023)
20-63741896-C-T		not specified	Uncertain significance (Dec 20, 2023)
20-63741998-C-T		not specified	Uncertain significance (Mar 02, 2023)
20-63742153-G-C		not specified	Uncertain significance (Apr 28, 2022)
20-63742199-A-G		not specified	Uncertain significance (May 05, 2023)
20-63742344-C-A		not specified	Uncertain significance (Dec 16, 2022)
20-63742464-C-T		not specified	Uncertain significance (Feb 16, 2023)
20-63742472-T-A		not specified	Uncertain significance (Apr 26, 2023)
20-63742479-G-T		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC2A4RG	protein_coding	protein_coding	ENST00000266077	8	3645

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.219	0.774	125066	1	140	125207	0.000563

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.188	181	188	0.961	0.0000123	2413
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00113	0.00109
Ashkenazi Jewish	0.00	0.00
East Asian	0.000125	0.000109
Finnish	0.000165	0.000139
European (Non-Finnish)	0.000391	0.000327
Middle Eastern	0.000125	0.000109
South Asian	0.00230	0.00206
Other	0.000887	0.000818

dbNSFP

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}.
• Pathway: AMP-activated Protein Kinase (AMPK) Signaling (Consensus)

Recessive Scores

• pRec: 0.213

Haploinsufficiency Scores

• pHI: 0.0952
• hipred: N
• hipred_score: 0.146
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.977

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription, DNA-templated
• Cellular component: nucleus;cytoplasm;nuclear speck
• Molecular function: DNA binding;DNA-binding transcription factor activity;metal ion binding