SLC26A1

solute carrier family 26 member 1, the group of Solute carrier family 26

Basic information

Region (hg38): 4:979072-993440

Links

ENSG00000145217 ∙ NCBI:10861 ∙ OMIM:610130 ∙ HGNC:10993 ∙ Uniprot:Q9H2B4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• nephrolithiasis susceptibility caused by SLC26A1 (Limited), mode of inheritance: AR
• nephrolithiasis susceptibility caused by SLC26A1 (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nephrolithiasis, calcium oxalate, 1	AR	Renal	Acute renal failure due to calcium oxalate nephrolithiasis has been described, and awareness may allow preventive measures and early diagnosis and management	Renal	27210743

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC26A1 gene.

• not provided (292 variants)
• Mucopolysaccharidosis type 1 (165 variants)
• Inborn genetic diseases (80 variants)
• Calcium oxalate nephrolithiasis (63 variants)
• Hurler syndrome (58 variants)
• not specified (14 variants)
• Mucopolysaccharidosis, MPS-I-H/S (8 variants)
• Mucopolysaccharidosis, MPS-I-S (5 variants)
• Mucopolysaccharidosis, MPS-I-S;Hurler syndrome;Mucopolysaccharidosis, MPS-I-H/S (5 variants)
• IDUA-related condition (4 variants)
• Hyperoxaluria (4 variants)
• SLC26A1-related condition (2 variants)
• Hurler syndrome;Mucopolysaccharidosis, MPS-I-H/S;Mucopolysaccharidosis, MPS-I-S (2 variants)
• Mucopolysaccharidosis (1 variants)
• Hereditary disease (1 variants)
• Abnormality of mucopolysaccharide metabolism (1 variants)
• Interstitial pneumonitis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC26A1 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	59	11	71
missense			142	20	6	168
nonsense			4	5		9
start loss						0
frameshift			4	16		20
inframe indel			3	2		5
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	30	16	64	73	17	200
Total	30	16	218	175	34

Highest pathogenic variant AF is 0.000578

Variants in SLC26A1

This is a list of pathogenic ClinVar variants found in the SLC26A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-979248-C-T			Benign (Jul 09, 2018)
4-979583-G-A			Benign (Jul 14, 2018)
4-986676-A-G			Benign (Jun 28, 2018)
4-986813-C-G			Likely benign (Jul 09, 2018)
4-986922-C-T			Likely benign (Jul 15, 2018)
4-987014-C-T		Mucopolysaccharidosis type 1 • Mucopolysaccharidosis, MPS-I-S;Hurler syndrome;Mucopolysaccharidosis, MPS-I-H/S	Uncertain significance (Aug 04, 2021)
4-987056-AGCCCCGCAGTCCCCGAGCACGCGTGGCCATGCGTCCCCTGC-A		Mucopolysaccharidosis type 1	Pathogenic (May 22, 2023)
4-987064-AGTCCCCGAGCACGCGTGGCCATGC-A		Mucopolysaccharidosis type 1	Pathogenic (Sep 10, 2023)
4-987083-C-T		Mucopolysaccharidosis type 1	Uncertain significance (Aug 14, 2020)
4-987085-A-C		Mucopolysaccharidosis type 1 • Hurler syndrome	Pathogenic (Mar 14, 2023)
4-987085-A-G		Mucopolysaccharidosis type 1	Pathogenic (Dec 08, 2023)
4-987086-T-C		Mucopolysaccharidosis type 1	Pathogenic (Aug 31, 2023)
4-987087-G-A		Hurler syndrome • Mucopolysaccharidosis type 1	Likely pathogenic (Jul 28, 2023)
4-987089-G-C		Mucopolysaccharidosis type 1	Uncertain significance (Sep 17, 2021)
4-987090-T-C		Mucopolysaccharidosis type 1	Likely benign (Jul 17, 2023)
4-987092-C-A		Mucopolysaccharidosis type 1	Uncertain significance (Feb 28, 2022)
4-987093-C-T		Mucopolysaccharidosis type 1	Likely benign (Apr 28, 2023)
4-987094-C-T		Mucopolysaccharidosis type 1	Likely benign (Apr 30, 2023)
4-987095-T-C		Mucopolysaccharidosis type 1 • Inborn genetic diseases	Conflicting classifications of pathogenicity (Jan 31, 2024)
4-987098-G-GC		Mucopolysaccharidosis type 1	Pathogenic (Aug 05, 2022)
4-987099-C-A		Mucopolysaccharidosis type 1	Likely benign (Feb 27, 2022)
4-987099-C-G		Mucopolysaccharidosis type 1	Likely benign (Nov 12, 2022)
4-987099-C-T		Mucopolysaccharidosis type 1	Likely benign (Mar 11, 2022)
4-987102-C-T		Mucopolysaccharidosis type 1	Likely benign (Dec 11, 2023)
4-987105-C-A		Mucopolysaccharidosis type 1	Likely benign (Mar 25, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC26A1	protein_coding	protein_coding	ENST00000361661	2	14368

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.06e-11	0.0457	125344	0	111	125455	0.000442

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.367	477	500	0.954	0.0000375	4329
Missense in Polyphen		182	196.63	0.92561		1883
Synonymous	-0.198	253	249	1.02	0.0000201	1644
Loss of Function	0.0412	17	17.2	0.989	9.84e-7	152

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000535	0.000517
Ashkenazi Jewish	0.00	0.00
East Asian	0.00408	0.00403
Finnish	0.0000520	0.0000462
European (Non-Finnish)	0.000103	0.0000971
Middle Eastern	0.00408	0.00403
South Asian	0.000349	0.000327
Other	0.000191	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates sulfate transport with high affinity (PubMed:12713736). Mediates oxalate transport (PubMed:12713736). Mediates bicarbonate transport (By similarity). Does not accept succinate as cosubstrate (By similarity). {ECO:0000250|UniProtKB:P45380, ECO:0000250|UniProtKB:P58735, ECO:0000269|PubMed:12713736}.
• Pathway: Transport and synthesis of PAPS;Metabolism of carbohydrates;Phase II - Conjugation of compounds;Glycosaminoglycan metabolism;Biological oxidations;Metabolism;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Cytosolic sulfonation of small molecules;Methionine and cysteine metabolism;Multifunctional anion exchangers (Consensus)

Recessive Scores

• pRec: 0.173

Intolerance Scores

• loftool: 0.0241
• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.73

Haploinsufficiency Scores

• pHI: 0.158
• hipred: N
• hipred_score: 0.251
• ghis: 0.672

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.848

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc26a1
• Phenotype: renal/urinary system phenotype; immune system phenotype; digestive/alimentary phenotype; liver/biliary system phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: ion transport;chloride transport;sulfate transport;bicarbonate transport;oxalate transport;3'-phosphoadenosine 5'-phosphosulfate biosynthetic process;sulfate transmembrane transport;chloride transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;integral component of membrane;basolateral plasma membrane
• Molecular function: secondary active sulfate transmembrane transporter activity;bicarbonate transmembrane transporter activity;chloride transmembrane transporter activity;sulfate transmembrane transporter activity;anion:anion antiporter activity;oxalate transmembrane transporter activity