SLC20A2

solute carrier family 20 member 2, the group of Solute carrier family 20

Basic information

Region (hg38): 8:42416474-42541926

Previous symbols: [ "MLVAR", "GLVR2" ]

Links

ENSG00000168575 ∙ NCBI:6575 ∙ OMIM:158378 ∙ HGNC:10947 ∙ Uniprot:Q08357 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• basal ganglia calcification, idiopathic, 1 (Strong), mode of inheritance: AD
• basal ganglia calcification, idiopathic, 1 (Strong), mode of inheritance: AD
• bilateral striopallidodentate calcinosis (Supportive), mode of inheritance: AD
• basal ganglia calcification, idiopathic, 1 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Basal ganglia calcification, idiopathic, 1	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	20552677; 22327515; 24463626

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC20A2 gene.

• not provided (190 variants)
• Idiopathic basal ganglia calcification 1 (111 variants)
• Inborn genetic diseases (18 variants)
• not specified (10 variants)
• SLC20A2-related condition (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC20A2 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			4	32	6	42
missense	3	6	73	5	4	91
nonsense	16	2				18
start loss			1			1
frameshift	13	4				17
inframe indel		1	3			4
splice donor/acceptor (+/-2bp)	5	5				10
splice region			7	3	1	11
non coding			18	20	25	63
Total	37	18	99	57	35

Highest pathogenic variant AF is 0.0000132

Variants in SLC20A2

This is a list of pathogenic ClinVar variants found in the SLC20A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-42416483-G-A		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 13, 2018)
8-42416734-C-G		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 12, 2018)
8-42416746-G-C		Idiopathic basal ganglia calcification 1	Benign (Jan 13, 2018)
8-42416877-G-A		Idiopathic basal ganglia calcification 1	Benign (Jan 12, 2018)
8-42416878-C-A		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 13, 2018)
8-42417005-C-T		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 13, 2018)
8-42417143-A-G		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 13, 2018)
8-42417233-C-A		Idiopathic basal ganglia calcification 1	Benign (Jan 12, 2018)
8-42417264-C-T		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 12, 2018)
8-42417265-G-A		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 13, 2018)
8-42417321-A-G		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 13, 2018)
8-42417394-T-C		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 13, 2018)
8-42417423-G-A		Idiopathic basal ganglia calcification 1	Benign (Jan 13, 2018)
8-42417442-T-C		Idiopathic basal ganglia calcification 1	Benign (Jan 13, 2018)
8-42417514-T-G		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 13, 2018)
8-42417540-T-G		Idiopathic basal ganglia calcification 1	Benign (Jan 12, 2018)
8-42417632-C-T		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 13, 2018)
8-42417679-C-A		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 12, 2018)
8-42417683-G-C		Idiopathic basal ganglia calcification 1	Benign (Jan 13, 2018)
8-42417690-T-A		Idiopathic basal ganglia calcification 1	Benign/Likely benign (Dec 24, 2018)
8-42417691-C-A		Idiopathic basal ganglia calcification 1	Benign/Likely benign (Dec 24, 2018)
8-42417733-G-A		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 12, 2018)
8-42417812-T-C			Uncertain significance (Dec 04, 2023)
8-42417828-A-T			Benign (Aug 17, 2023)
8-42417829-T-C		Idiopathic basal ganglia calcification 1	Uncertain significance (May 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC20A2	protein_coding	protein_coding	ENST00000342228	10	123077

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.965	0.0346	125736	0	10	125746	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.63	261	411	0.635	0.0000257	4193
Missense in Polyphen		91	162.83	0.55885		1661
Synonymous	-1.46	210	185	1.14	0.0000140	1389
Loss of Function	4.21	4	28.1	0.142	0.00000153	303

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000933	0.0000933
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sodium-phosphate symporter which seems to play a fundamental housekeeping role in phosphate transport by absorbing phosphate from interstitial fluid for normal cellular functions such as cellular metabolism, signal transduction, and nucleic acid and lipid synthesis. In vitro, sodium-dependent phosphate uptake is not siginificantly affected by acidic and alkaline conditions, however sodium-independent phosphate uptake occurs at acidic conditions. May play a role in extracellular matrix, cartilage and vascular calcification. Functions as a retroviral receptor and confers human cells susceptibility to infection to amphotropic murine leukemia virus (A-MuLV), 10A1 murine leukemia virus (10A1 MLV) and some feline leukemia virus subgroup B (FeLV-B) variants. {ECO:0000269|PubMed:11435563, ECO:0000269|PubMed:12205090, ECO:0000269|PubMed:15955065, ECO:0000269|PubMed:16790504, ECO:0000269|PubMed:8302848}.
• Disease: DISEASE: Basal ganglia calcification, idiopathic, 1 (IBGC1) [MIM:213600]: A form of basal ganglia calcification, an autosomal dominant condition characterized by symmetric calcification in the basal ganglia and other brain regions. Affected individuals can either be asymptomatic or show a wide spectrum of neuropsychiatric symptoms, including parkinsonism, dystonia, tremor, ataxia, dementia, psychosis, seizures, and chronic headache. Serum levels of calcium, phosphate, alkaline phosphatase and parathyroid hormone are normal. The neuropathological hallmark of the disease is vascular and pericapillary calcification, mainly of calcium phosphate, in the affected brain areas. {ECO:0000269|PubMed:15955065, ECO:0000269|PubMed:22327515, ECO:0000269|PubMed:23334463, ECO:0000269|PubMed:23406454, ECO:0000269|PubMed:23939468, ECO:0000269|PubMed:24065723, ECO:0000269|PubMed:24463626, ECO:0000269|PubMed:25284758}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Sodium-coupled phosphate cotransporters (Consensus)

Recessive Scores

• pRec: 0.176

Intolerance Scores

• loftool: 0.0451
• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.67

Haploinsufficiency Scores

• pHI: 0.588
• hipred: Y
• hipred_score: 0.728
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.115

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc20a2
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); craniofacial phenotype; homeostasis/metabolism phenotype; skeleton phenotype; embryo phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system 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); neoplasm; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; immune system phenotype

Gene ontology

• Biological process: ion transport;phosphate ion transmembrane transport;sodium ion transmembrane transport;sodium-dependent phosphate transport;viral entry into host cell
• Cellular component: plasma membrane;integral component of plasma membrane;membrane;extracellular exosome
• Molecular function: virus receptor activity;inorganic phosphate transmembrane transporter activity;sodium:phosphate symporter activity;sodium:inorganic phosphate symporter activity;sodium-dependent phosphate transmembrane transporter activity;signaling receptor activity