SLC16A12

solute carrier family 16 member 12, the group of Solute carrier family 16

Basic information

Region (hg38): 10:89430299-89556641

Links

ENSG00000152779 ∙ NCBI:387700 ∙ OMIM:611910 ∙ HGNC:23094 ∙ Uniprot:Q6ZSM3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• juvenile cataract-microcornea-renal glucosuria syndrome (Strong), mode of inheritance: AD
• juvenile cataract-microcornea-renal glucosuria syndrome (Limited), mode of inheritance: Unknown
• juvenile cataract-microcornea-renal glucosuria syndrome (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cataract 47	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	Biochemical; Renal	17458810; 18304496

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC16A12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC16A12 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				8		8
missense		1	32	4	1	38
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1	6	9	16
Total	0	1	34	18	10

Variants in SLC16A12

This is a list of pathogenic ClinVar variants found in the SLC16A12 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-89432879-G-T			Likely benign (Jun 28, 2018)
10-89432902-A-T			Benign (Jul 05, 2019)
10-89433073-G-T			Uncertain significance (May 22, 2023)
10-89433096-C-T		not specified	Uncertain significance (Jan 08, 2024)
10-89433129-T-C		not specified • SLC16A12-related disorder	Uncertain significance (Sep 16, 2021)
10-89433134-A-C			Uncertain significance (May 24, 2022)
10-89433149-G-A		Juvenile cataract-microcornea-renal glucosuria syndrome	Uncertain significance (Apr 30, 2024)
10-89433159-T-C		Juvenile cataract-microcornea-renal glucosuria syndrome	Uncertain significance (May 17, 2024)
10-89433171-G-T		not specified	Uncertain significance (Nov 20, 2024)
10-89433174-T-G			Uncertain significance (Oct 03, 2023)
10-89433200-T-C		not specified	Likely benign (Jul 14, 2024)
10-89433217-C-T		not specified • Juvenile cataract-microcornea-renal glucosuria syndrome	Uncertain significance (Feb 12, 2024)
10-89433261-A-G		Juvenile cataract-microcornea-renal glucosuria syndrome	Uncertain significance (Jun 04, 2024)
10-89433263-A-G		not specified	Uncertain significance (Mar 29, 2022)
10-89433297-T-G		not specified	Uncertain significance (Aug 12, 2021)
10-89433324-G-A		not specified	Likely benign (Aug 17, 2022)
10-89433565-T-C			Benign (Jun 28, 2018)
10-89436093-C-A		Juvenile cataract-microcornea-renal glucosuria syndrome	Uncertain significance (Mar 30, 2024)
10-89436093-C-T		Juvenile cataract-microcornea-renal glucosuria syndrome	Uncertain significance (Jun 01, 2024)
10-89436108-C-T		Juvenile cataract-microcornea-renal glucosuria syndrome	Uncertain significance (Apr 05, 2024)
10-89436118-C-T		SLC16A12-related disorder	Likely benign (Oct 21, 2022)
10-89436129-A-G			Likely benign (Aug 10, 2023)
10-89436131-G-C		Juvenile cataract-microcornea-renal glucosuria syndrome • SLC16A12-related disorder	Benign/Likely benign (Apr 08, 2022)
10-89436141-C-T		not specified	Uncertain significance (Oct 01, 2024)
10-89436201-A-G		Juvenile cataract-microcornea-renal glucosuria syndrome	Uncertain significance (May 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC16A12	protein_coding	protein_coding	ENST00000371790	6	126348

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.493	0.507	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.951	233	278	0.839	0.0000143	3323
Missense in Polyphen		84	120.48	0.69722		1457
Synonymous	0.545	98	105	0.932	0.00000570	1071
Loss of Function	3.20	4	19.1	0.209	8.15e-7	253

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000621	0.0000615
Middle Eastern	0.000326	0.000326
South Asian	0.0000653	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Proton-linked monocarboxylate transporter that mediates creatine transport across the plasma membrane. {ECO:0000269|PubMed:23578822}.
• Pathway: Glycosphingolipid metabolism;Glycerophospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.726
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.272
• hipred: N
• hipred_score: 0.289
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0466

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc16a12

Gene ontology

• Biological process: monocarboxylic acid transport;creatine transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: creatine transmembrane transporter activity;monocarboxylic acid transmembrane transporter activity;symporter activity