SLC16A4

solute carrier family 16 member 4, the group of Solute carrier family 16

Basic information

Region (hg38): 1:110362850-110391082

Links

ENSG00000168679 ∙ NCBI:9122 ∙ OMIM:603878 ∙ HGNC:10925 ∙ Uniprot:O15374 ∙ 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 SLC16A4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC16A4 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			17		1	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	1

Variants in SLC16A4

This is a list of pathogenic ClinVar variants found in the SLC16A4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-110363793-G-C		not specified	Likely benign (Jun 23, 2023)
1-110363861-C-A		not specified	Uncertain significance (Feb 09, 2022)
1-110375503-T-C		not specified	Uncertain significance (Jul 25, 2023)
1-110375538-C-G		not specified	Uncertain significance (Jan 19, 2022)
1-110376967-A-T		not specified	Uncertain significance (Jun 11, 2024)
1-110377075-G-A		not specified	Uncertain significance (Dec 18, 2023)
1-110378887-G-T		not specified	Uncertain significance (Jan 31, 2023)
1-110379024-A-G		not specified	Uncertain significance (Mar 16, 2024)
1-110379105-C-T		not specified	Uncertain significance (Jan 16, 2024)
1-110379182-T-G		not specified	Uncertain significance (May 23, 2023)
1-110379221-T-G		not specified	Uncertain significance (Jul 14, 2021)
1-110379227-C-A		not specified	Uncertain significance (May 18, 2023)
1-110379245-C-T		not specified	Uncertain significance (Apr 25, 2023)
1-110379308-C-T		not specified	Uncertain significance (Apr 27, 2023)
1-110379315-G-C		not specified	Uncertain significance (Mar 20, 2024)
1-110379330-C-T			Benign (Apr 05, 2018)
1-110379347-A-C		not specified	Uncertain significance (Jan 09, 2024)
1-110381059-A-G		not specified	Uncertain significance (Jul 20, 2021)
1-110381654-G-A		not specified	Uncertain significance (Dec 20, 2021)
1-110382845-C-T		not specified	Uncertain significance (Mar 06, 2023)
1-110382857-A-T		not specified	Uncertain significance (Apr 22, 2022)
1-110389272-C-T		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC16A4	protein_coding	protein_coding	ENST00000369779	8	28235

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.67e-8	0.770	125640	0	108	125748	0.000430

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.879	215	254	0.845	0.0000119	3179
Missense in Polyphen		76	91.577	0.8299		1138
Synonymous	0.444	86	91.4	0.941	0.00000444	953
Loss of Function	1.38	14	20.8	0.673	9.78e-7	251

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00470	0.00469
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000794	0.0000791
Middle Eastern	0.000164	0.000163
South Asian	0.000398	0.000392
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Proton-linked monocarboxylate transporter. Catalyzes the rapid transport across the plasma membrane of many monocarboxylates such as lactate, pyruvate, branched-chain oxo acids derived from leucine, valine and isoleucine, and the ketone bodies acetoacetate, beta-hydroxybutyrate and acetate (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0891

Intolerance Scores

• loftool: 0.777
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.59

Haploinsufficiency Scores

• pHI: 0.0821
• hipred: N
• hipred_score: 0.457
• ghis: 0.459

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.737

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc16a4

Gene ontology

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