SLC14A2

solute carrier family 14 member 2, the group of Solute carrier family 14

Basic information

Region (hg38): 18:45212994-45683688

Links

ENSG00000132874 ∙ NCBI:8170 ∙ OMIM:601611 ∙ HGNC:10919 ∙ Uniprot:Q15849 ∙ 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 SLC14A2 gene.

• Inborn genetic diseases (37 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC14A2 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		1
missense			37		1	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	1	1

Variants in SLC14A2

This is a list of pathogenic ClinVar variants found in the SLC14A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-45624728-G-A		not specified	Uncertain significance (Apr 04, 2023)
18-45624751-C-A		not specified	Uncertain significance (Oct 12, 2022)
18-45624761-A-G		not specified	Uncertain significance (Dec 13, 2023)
18-45624768-C-T		not specified	Uncertain significance (Jul 05, 2023)
18-45625689-C-T		not specified	Uncertain significance (Apr 21, 2022)
18-45625690-G-A		not specified	Uncertain significance (Mar 11, 2024)
18-45625698-A-G		not specified	Uncertain significance (Mar 07, 2023)
18-45625832-C-T			Likely benign (Apr 01, 2023)
18-45626970-C-A		not specified	Uncertain significance (Apr 07, 2022)
18-45627027-A-G		not specified	Uncertain significance (Aug 02, 2023)
18-45627029-C-A		not specified	Uncertain significance (Mar 02, 2023)
18-45627041-C-G		not specified	Uncertain significance (Feb 13, 2023)
18-45627096-G-T		not specified	Uncertain significance (Dec 11, 2023)
18-45627111-T-G		not specified	Uncertain significance (Dec 20, 2023)
18-45627114-C-T		not specified	Uncertain significance (Sep 16, 2021)
18-45632384-G-A		not specified	Uncertain significance (Oct 28, 2023)
18-45632471-A-C		not specified	Uncertain significance (Jan 31, 2023)
18-45637127-T-C		not specified	Uncertain significance (Sep 23, 2023)
18-45644047-C-T		not specified	Uncertain significance (Mar 01, 2023)
18-45644150-G-T		not specified	Uncertain significance (Oct 12, 2021)
18-45644152-C-A		not specified	Uncertain significance (Aug 09, 2021)
18-45644154-C-A		not specified	Uncertain significance (May 17, 2023)
18-45644160-G-A			Benign (Jul 10, 2017)
18-45663836-C-T		not specified	Uncertain significance (Jul 26, 2022)
18-45663887-C-G		not specified	Uncertain significance (Feb 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC14A2	protein_coding	protein_coding	ENST00000255226	19	470113

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.06e-17	0.399	125523	1	224	125748	0.000895

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.138	534	525	1.02	0.0000287	5958
Missense in Polyphen		139	152.95	0.90882		1766
Synonymous	-0.298	232	226	1.03	0.0000146	1890
Loss of Function	1.66	33	45.0	0.733	0.00000205	504

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00314	0.00314
Ashkenazi Jewish	0.00	0.00
East Asian	0.00167	0.00163
Finnish	0.00208	0.00203
European (Non-Finnish)	0.000679	0.000668
Middle Eastern	0.00167	0.00163
South Asian	0.000327	0.000327
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Specialized low-affinity vasopressin-regulated urea transporter. Mediates rapid transepithelial urea transport across the inner medullary collecting duct and plays a major role in the urinary concentrating mechanism. {ECO:0000269|PubMed:11502588, ECO:0000269|PubMed:8647271}.
• Pathway: Polythiazide Action Pathway;Methyclothiazide Action Pathway;Bumetanide Action Pathway;Spironolactone Action Pathway;Eplerenone Action Pathway;Triamterene Action Pathway;Amiloride Action Pathway;Ethacrynic Acid Action Pathway;Quinethazone Action Pathway;Bendroflumethiazide Action Pathway;Chlorthalidone Action Pathway;Trichlormethiazide Action Pathway;Iminoglycinuria;Lysinuric Protein Intolerance;Blue diaper syndrome;Lysinuric protein intolerance (LPI);Cystinuria;Indapamide Action Pathway;Furosemide Action Pathway;Torsemide Action Pathway;Hartnup Disorder;Glucose Transporter Defect (SGLT2);Kidney Function;Glucose Transporter Defect (SGLT2);Metolazone Action Pathway;Hydrochlorothiazide Action Pathway;Cyclothiazide Action Pathway;Hydroflumethiazide Action Pathway;Chlorothiazide Action Pathway;Amine compound SLC transporters;Purine metabolism;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.179

Intolerance Scores

• loftool: 0.877
• rvis_EVS: 0.28
• rvis_percentile_EVS: 70.78

Haploinsufficiency Scores

• pHI: 0.142
• hipred: N
• hipred_score: 0.177
• ghis: 0.402

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.225

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc14a2
• Phenotype: homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; renal/urinary system phenotype; reproductive 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: slc14a2
• Affected structure: urea transport
• Phenotype tag: abnormal
• Phenotype quality: decreased rate

Gene ontology

• Biological process: urea transport;transmembrane transport;urea transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;membrane;integral component of membrane;apical plasma membrane
• Molecular function: urea transmembrane transporter activity;urea channel activity;cell adhesion molecule binding