SLC52A2

solute carrier family 52 member 2, the group of Solute carrier family 52

Basic information

Region (hg38): 8:144333956-144361286

Previous symbols: [ "GPR172A" ]

Links

ENSG00000185803 ∙ NCBI:79581 ∙ OMIM:607882 ∙ HGNC:30224 ∙ Uniprot:Q9HAB3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• brown-Vialetto-van Laere syndrome 2 (Strong), mode of inheritance: AR
• brown-Vialetto-van Laere syndrome 2 (Definitive), mode of inheritance: AR
• brown-Vialetto-van Laere syndrome 2 (Strong), mode of inheritance: AR
• brown-Vialetto-van Laere syndrome 2 (Strong), mode of inheritance: AR
• brown-Vialetto-van Laere syndrome 2 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Brown-Vialetto-Van Laere syndrome 2	AR	Audiologic/Otolaryngologic; Biochemical	Individuals may manifest with progressive neurological dysfunction, and there is evidence that medical/dietary management (with high-dose riboflavin therapy) may be beneficial; Awareness of the potential for hearing loss may allow early interventions related to speech and language development	Audiologic/Otolaryngologic; Biochemical; Musculoskeletal; Neurologic; Ophthalmologic	22740598; 23107375; 23243084; 30343981

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC52A2 gene.

• Brown-Vialetto-van Laere syndrome 2 (401 variants)
• Inborn genetic diseases (104 variants)
• not provided (79 variants)
• not specified (27 variants)
• Brown-Vialetto-van Laere syndrome 1 (2 variants)
• Sensorineural hearing loss disorder (1 variants)
• SLC52A2-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC52A2 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			7	133	5	145
missense	3	9	215	3		230
nonsense	5					5
start loss						0
frameshift	8	2	1			11
inframe indel		1	3			4
splice donor/acceptor (+/-2bp)		1	1			2
splice region			4	7	1	12
non coding			3	23	5	31
Total	16	13	230	159	10

Highest pathogenic variant AF is 0.0000788

Variants in SLC52A2

This is a list of pathogenic ClinVar variants found in the SLC52A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-144333966-G-A		not specified	Uncertain significance (Oct 25, 2023)
8-144334001-C-T			Likely benign (Jan 01, 2023)
8-144334028-C-G		not specified	Uncertain significance (Jul 26, 2022)
8-144334084-C-T		not specified	Uncertain significance (Feb 06, 2023)
8-144334111-G-T		not specified	Uncertain significance (Jan 09, 2024)
8-144354670-G-A		Epidermolysis bullosa simplex with nail dystrophy	Uncertain significance (-)
8-144355538-G-C		not specified	Uncertain significance (Dec 07, 2021)
8-144355593-G-A		not specified	Uncertain significance (Sep 16, 2021)
8-144355595-T-C		not specified	Uncertain significance (Sep 16, 2021)
8-144355598-G-A		not specified	Uncertain significance (Jun 14, 2022)
8-144355635-C-T		not specified	Uncertain significance (Jun 22, 2023)
8-144355646-T-C		not specified	Uncertain significance (Oct 16, 2023)
8-144355652-A-C		not specified	Uncertain significance (Feb 28, 2024)
8-144355987-C-T		not specified	Uncertain significance (Jan 26, 2022)
8-144355989-C-T		not specified	Uncertain significance (Jun 21, 2023)
8-144355990-G-A		not specified	Uncertain significance (Jul 14, 2021)
8-144356044-T-C		not specified	Likely benign (Aug 10, 2021)
8-144356095-C-T		not specified	Uncertain significance (Mar 27, 2023)
8-144356097-C-T		not specified	Uncertain significance (Sep 07, 2022)
8-144356148-C-T		not specified	Uncertain significance (Sep 22, 2022)
8-144356153-C-G		not specified	Uncertain significance (Apr 14, 2023)
8-144356173-G-A		not specified	Uncertain significance (Jun 29, 2022)
8-144356181-G-A		not specified	Likely benign (Dec 03, 2021)
8-144356205-T-C		not specified	Uncertain significance (Jan 19, 2022)
8-144356303-G-A		not specified	Uncertain significance (Aug 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC52A2	protein_coding	protein_coding	ENST00000532887	4	7138

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00248	0.936	125713	0	21	125734	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.845	300	262	1.15	0.0000164	2740
Missense in Polyphen		87	85.816	1.0138		1015
Synonymous	-3.13	176	131	1.35	0.00000907	1106
Loss of Function	1.63	6	12.1	0.494	5.28e-7	134

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.0000998	0.0000992
East Asian	0.0000545	0.0000544
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.0000978	0.0000967
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

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) and flavin mononucleotide (FMN). 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:19307586, ECO:0000269|PubMed:20463145, ECO:0000269|PubMed:22864630, ECO:0000269|PubMed:23243084, ECO:0000269|PubMed:24253200, ECO:0000269|PubMed:27702554}.
• Pathway: Metabolism;Vitamin B2 (riboflavin) metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• rvis_EVS: -0.93
• rvis_percentile_EVS: 9.55

Haploinsufficiency Scores

• pHI: 0.154
• hipred: N
• hipred_score: 0.112
• ghis: 0.610

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	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Slc52a2
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; hearing/vestibular/ear phenotype

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;protein binding;riboflavin transmembrane transporter activity