SLC5A9

solute carrier family 5 member 9, the group of Solute carrier family 5

Basic information

Region (hg38): 1:48222685-48248644

Links

ENSG00000117834 ∙ NCBI:200010 ∙ OMIM:620216 ∙ HGNC:22146 ∙ Uniprot:Q2M3M2 ∙ 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 SLC5A9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC5A9 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						0
missense			58	3	1	62
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	60	3	1

Variants in SLC5A9

This is a list of pathogenic ClinVar variants found in the SLC5A9 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-48222781-C-T		SLC5A9-related disorder	Likely benign (Jun 18, 2019)
1-48222785-G-T		not specified	Uncertain significance (Mar 16, 2022)
1-48222797-A-G		not specified	Uncertain significance (Jan 08, 2024)
1-48222839-G-A		not specified	Uncertain significance (Mar 01, 2023)
1-48222896-T-C		not specified	Uncertain significance (Jun 10, 2024)
1-48224734-G-A		not specified	Uncertain significance (Dec 17, 2023)
1-48224752-T-C		not specified	Uncertain significance (Nov 12, 2024)
1-48224754-G-A		not specified	Uncertain significance (Jan 02, 2024)
1-48228851-T-C		not specified	Uncertain significance (Apr 24, 2024)
1-48228875-A-T		not specified	Uncertain significance (Aug 30, 2021)
1-48228892-T-C		not specified	Uncertain significance (Oct 03, 2022)
1-48228922-G-A		SLC5A9-related disorder	Benign (Apr 30, 2020)
1-48228927-C-G		SLC5A9-related disorder	Likely benign (Jan 05, 2024)
1-48228931-G-C		not specified	Uncertain significance (Mar 31, 2024)
1-48228946-G-A		not specified	Uncertain significance (Dec 11, 2023)
1-48228955-G-A			Uncertain significance (May 30, 2017)
1-48229118-T-A		not specified	Uncertain significance (May 25, 2022)
1-48229133-G-A		not specified	Uncertain significance (Jun 22, 2024)
1-48229154-G-A		not specified	Likely benign (May 18, 2022)
1-48229172-T-C		not specified	Uncertain significance (Apr 24, 2024)
1-48229304-C-T		SLC5A9-related disorder	Likely benign (Jul 16, 2019)
1-48229325-G-A		SLC5A9-related disorder	Benign (Feb 20, 2019)
1-48229409-G-A		SLC5A9-related disorder	Benign (Oct 23, 2019)
1-48229421-G-T		not specified	Uncertain significance (Jan 17, 2024)
1-48229436-C-G		not specified	Uncertain significance (Aug 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC5A9	protein_coding	protein_coding	ENST00000236495	15	25960

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.21e-27	0.000114	93221	2804	29723	125748	0.139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.802	380	427	0.891	0.0000244	4541
Missense in Polyphen		159	185.42	0.85753		2033
Synonymous	0.154	173	176	0.985	0.0000110	1490
Loss of Function	-0.229	39	37.5	1.04	0.00000204	360

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.225	0.224
Ashkenazi Jewish	0.155	0.154
East Asian	0.00979	0.00978
Finnish	0.162	0.161
European (Non-Finnish)	0.164	0.162
Middle Eastern	0.00979	0.00978
South Asian	0.188	0.187
Other	0.156	0.154

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in sodium-dependent transport of D-mannose, D- glucose and D-fructose. {ECO:0000269|PubMed:15607332}.
• Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway;SLC-mediated transmembrane transport;Transport of small molecules;Fructose and mannose metabolism;Galactose metabolism;Cellular hexose transport (Consensus)

Intolerance Scores

• loftool: 0.0795
• rvis_EVS: 1.14
• rvis_percentile_EVS: 92.37

Haploinsufficiency Scores

• pHI: 0.157
• hipred: N
• hipred_score: 0.197
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.289

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc5a9

Gene ontology

• Biological process: sodium ion transport;hexose transmembrane transport;glucose transmembrane transport
• Cellular component: plasma membrane;integral component of membrane;extracellular exosome
• Molecular function: low-affinity glucose:sodium symporter activity;glucose:sodium symporter activity