SLC52A1

solute carrier family 52 member 1, the group of Solute carrier family 52

Basic information

Region (hg38): 17:5032599-5052009

Previous symbols: [ "GPR172B" ]

Links

ENSG00000132517 ∙ NCBI:55065 ∙ OMIM:607883 ∙ HGNC:30225 ∙ Uniprot:Q9NWF4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• maternal riboflavin deficiency (Supportive), mode of inheritance: AD
• maternal riboflavin deficiency (Limited), mode of inheritance: AD
• ariboflavinosis (Limited), mode of inheritance: Unknown
• maternal riboflavin deficiency (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Riboflavin deficiency	AD	Biochemical	One individual with a heterozygous deletion has been reported, and this was postulated as contributing to transient neonatal-onset glutaric aciduria Type 2 in this individual's offspring,which was reported as being effectively treated by riboflavin therapy	Biochemical; Neurologic	17689999; 21089064; 23107375
Theoretically, biallelic variants could contribute to disease similar to that arising from variants in SLC52A2 or SLC52A3

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC52A1 gene.

• Ariboflavinosis (148 variants)
• not provided (18 variants)
• Inborn genetic diseases (18 variants)
• Maternal riboflavin deficiency (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC52A1 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			3	41	4	48
missense			86	3	5	94
nonsense			1			1
start loss	1					1
frameshift			8			8
inframe indel			2	1		3
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				4	10	14
Total	1	0	100	49	19

Variants in SLC52A1

This is a list of pathogenic ClinVar variants found in the SLC52A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-5032883-A-G			Benign (Jul 31, 2018)
17-5032964-C-T		Ariboflavinosis	Uncertain significance (Jul 24, 2023)
17-5032967-C-T		Ariboflavinosis	Uncertain significance (Mar 15, 2019)
17-5032975-T-C		Ariboflavinosis	Likely benign (Sep 07, 2022)
17-5032983-C-G		Ariboflavinosis • SLC52A1-related disorder	Likely benign (Jan 11, 2024)
17-5032987-T-C		Ariboflavinosis	Likely benign (Sep 21, 2023)
17-5032990-G-C		Ariboflavinosis	Uncertain significance (Feb 25, 2021)
17-5033011-GC-G		Ariboflavinosis	Uncertain significance (May 22, 2023)
17-5033015-G-C		Ariboflavinosis	Uncertain significance (Dec 18, 2021)
17-5033026-C-A		Ariboflavinosis	Uncertain significance (Apr 29, 2023)
17-5033031-C-T		Ariboflavinosis	Uncertain significance (Jul 05, 2022)
17-5033034-C-T		Ariboflavinosis	Uncertain significance (Jun 03, 2023)
17-5033041-A-G		Ariboflavinosis	Benign (Jul 12, 2023)
17-5033041-A-T		Ariboflavinosis • SLC52A1-related disorder	Benign (Feb 01, 2024)
17-5033056-T-C		Ariboflavinosis	Likely benign (Jul 19, 2022)
17-5033064-C-T		Ariboflavinosis	Uncertain significance (Aug 16, 2022)
17-5033075-G-T		Ariboflavinosis	Uncertain significance (Aug 08, 2022)
17-5033078-A-G		Ariboflavinosis	Uncertain significance (Sep 28, 2023)
17-5033087-G-A		Ariboflavinosis • not specified	Uncertain significance (Nov 17, 2023)
17-5033090-C-T		not specified	Uncertain significance (Jun 30, 2023)
17-5033091-G-C		not specified	Uncertain significance (Jan 30, 2024)
17-5033094-C-T		Ariboflavinosis	Uncertain significance (Jun 02, 2023)
17-5033116-T-G		Ariboflavinosis	Likely benign (Jul 23, 2022)
17-5033117-G-T		Ariboflavinosis	Uncertain significance (Dec 12, 2021)
17-5033122-C-CT		Ariboflavinosis	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC52A1	protein_coding	protein_coding	ENST00000424747	4	19410

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000352	0.366	125646	0	101	125747	0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0538	251	253	0.990	0.0000137	2781
Missense in Polyphen		89	84.03	1.0591		1032
Synonymous	0.0658	121	122	0.992	0.00000694	1103
Loss of Function	0.388	9	10.3	0.870	4.44e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00272	0.00272
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.000265	0.000237
Middle Eastern	0.000109	0.000109
South Asian	0.000435	0.000425
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Riboflavin transporter. Riboflavin transport is Na(+)- independent but moderately pH-sensitive. Activity is strongly inhibited by riboflavin analogs, such as lumiflavin. Weakly inhibited by flavin adenine dinucleotide (FAD). In case of infection by retroviruses, acts as a cell receptor to retroviral envelopes similar to the porcine endogenous retrovirus (PERV-A). {ECO:0000269|PubMed:12740431, ECO:0000269|PubMed:20463145}.
• Pathway: Metabolism;Vitamin B2 (riboflavin) metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors (Consensus)

Recessive Scores

• pRec: 0.0920

Intolerance Scores

• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.66

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.139
• ghis: 0.432

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: riboflavin metabolic process;riboflavin transport;viral entry into host cell
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: virus receptor activity;riboflavin transmembrane transporter activity