SLC20A1

solute carrier family 20 member 1, the group of Solute carrier family 20

Basic information

Region (hg38): 2:112645939-112663825

Previous symbols: [ "GLVR1" ]

Links

ENSG00000144136 ∙ NCBI:6574 ∙ OMIM:137570 ∙ HGNC:10946 ∙ Uniprot:Q8WUM9 ∙ 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 SLC20A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC20A1 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	1	5
missense			24		1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				1		1
Total	0	0	24	5	2

Variants in SLC20A1

This is a list of pathogenic ClinVar variants found in the SLC20A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-112646850-A-G		not specified	Uncertain significance (Apr 06, 2023)
2-112646883-G-A		not specified	Uncertain significance (Apr 08, 2022)
2-112646904-A-G		not specified	Uncertain significance (Dec 17, 2023)
2-112647088-A-C		not specified	Uncertain significance (Aug 02, 2021)
2-112647115-A-G		not specified	Uncertain significance (Dec 14, 2023)
2-112647123-C-G		not specified	Uncertain significance (Apr 12, 2023)
2-112647131-G-A		SLC20A1-related disorder	Benign (Oct 17, 2019)
2-112647397-A-C			Likely benign (Nov 01, 2022)
2-112647400-T-C		SLC20A1-related disorder	Likely benign (Aug 13, 2019)
2-112647655-A-C		not specified	Uncertain significance (Mar 18, 2024)
2-112652699-C-T		SLC20A1-related disorder	Likely benign (Apr 10, 2019)
2-112652703-C-G		not specified	Uncertain significance (Dec 14, 2023)
2-112652727-G-A		not specified	Uncertain significance (May 20, 2024)
2-112652754-C-T		not specified	Uncertain significance (May 27, 2022)
2-112652768-C-G		not specified	Uncertain significance (Jul 13, 2022)
2-112652778-T-C		not specified	Uncertain significance (Oct 25, 2023)
2-112657128-G-T		not specified	Uncertain significance (Nov 21, 2022)
2-112657137-A-G		not specified	Uncertain significance (Sep 12, 2023)
2-112657167-C-T		not specified	Uncertain significance (Oct 06, 2022)
2-112658954-C-A		not specified	Uncertain significance (Dec 22, 2023)
2-112658962-G-A		not specified	Uncertain significance (Mar 24, 2023)
2-112659103-G-C		SLC20A1-related disorder	Likely benign (May 08, 2019)
2-112659206-G-A			Benign (Oct 10, 2018)
2-112659295-C-T			Likely benign (Nov 01, 2022)
2-112659376-C-T		SLC20A1-related disorder	Likely benign (Aug 14, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC20A1	protein_coding	protein_coding	ENST00000272542	10	17971

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0672	0.933	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.85	278	379	0.733	0.0000194	4431
Missense in Polyphen		75	143.04	0.52435		1639
Synonymous	0.219	137	140	0.976	0.00000757	1383
Loss of Function	3.70	8	29.8	0.269	0.00000170	331

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00129	0.00129
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000794	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sodium-phosphate symporter which plays a fundamental housekeeping role in phosphate transport, such as absorbing phosphate from interstitial fluid for normal cellular functions such as cellular metabolism, signal transduction, and nucleic acid and lipid synthesis. May play a role in extracellular matrix and cartilage calcification as well as in vascular calcification. {ECO:0000269|PubMed:11009570, ECO:0000269|PubMed:7929240, ECO:0000269|PubMed:7966619, ECO:0000269|PubMed:8041748}.
• 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: 0.170

Intolerance Scores

• loftool: 0.141
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.813
• hipred: Y
• hipred_score: 0.625
• ghis: 0.514

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0621

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc20a1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region 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); immune system phenotype; skeleton phenotype; embryo phenotype; liver/biliary system phenotype; 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); normal phenotype

Gene ontology

• Biological process: phosphate-containing compound metabolic process;ion transport;biomineral tissue development;phosphate ion transmembrane transport;sodium ion transmembrane transport;positive regulation of I-kappaB kinase/NF-kappaB signaling;sodium-dependent phosphate transport
• Cellular component: plasma membrane;integral component of plasma membrane;membrane
• Molecular function: inorganic phosphate transmembrane transporter activity;high-affinity inorganic phosphate:sodium symporter activity;sodium:phosphate symporter activity;sodium:inorganic phosphate symporter activity;sodium-dependent phosphate transmembrane transporter activity;signaling receptor activity