SLC16A7

protein-coding

solute carrier family 16 member 7, the group of Solute carrier family 16

Gene summary

This gene is a member of the monocarboxylate transporter family. Members in this family transport metabolites, such as lactate, pyruvate, and ketone bodies. The protein encoded by this gene catalyzes the proton-linked transport of monocarboxylates and has the highest affinity for pyruvate. This protein has been reported to be more highly expressed in prostate and colorectal cancer specimens when compared to control specimens. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2012]

MANE transcript

NM_001270623.2

Inheritance

—

ClinVar variants

U:69B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.42

Max pathogenic AF

—

Genomic locus

chr12:59,596,029-59,789,855

External References & Databases

Ensembl (ENSG00000118596)

Transcript & Mutation Effects

hg38 • Region Span ~193.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC16A7 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 71

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001270623.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	1 clinvar	2
missense			68 clinvar	3 clinvar	1 clinvar	72
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	69	4	2	75

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 64 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001270623.2	RefSeq	NP_001257552.1	4	MANE Select
ENST00000547379.6	Ensembl	ENSP00000448071.1	4	MANE Select
NM_001270622.2	RefSeq	NP_001257551.1	4	Standard
NM_004731.5	RefSeq	NP_004722.2	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Bile salt and organic anion SLC transporters
Glycolysis and Gluconeogenesis
Proton-coupled monocarboxylate transport
Transport of bile salts and organic acids, metal ions and amine compounds
SLC-mediated transmembrane transport

Biological Process

monocarboxylic acid transport
lactate transmembrane transport
pyruvate transmembrane transport

Molecular Function

pyruvate secondary active transmembrane transporter activity
monocarboxylic acid transmembrane transporter activity
lactate transmembrane transporter activity
symporter activity
pyruvate transmembrane transporter activity

Cellular Component

plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000261187
Coding exons: 4
Length: 186548
Individuals with no LoFs: 125700
Homozygous LoFs: 0
Heterozygous LoFs: 35
Defined: 125735
p: 0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.279	246	259	0.951	0.0000128	3105
Missense (PolyPhen)		103	121.97	0.8445		1442
Synonymous	0.744	88	97.3	0.904	0.00000534	961
Loss of Function	2.04	6	14.3	0.419	8.31e-7	175

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00027	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.00016	0.00016	rare
Other	0.00036	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Proton-coupled 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. Functions as high-affinity pyruvate transporter. {ECO:0000269|PubMed:9786900}.;

Recessive Scores

pRec: 0.154

Intolerance Scores

LoFtool: 0.697
RVIS EVS: 0.37
RVIS percentile EVS: 75.43

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.336

Gene Damage Prediction

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