SLC6A16

protein-coding

solute carrier family 6 member 16, the group of MicroRNA protein coding host genes|Solute carrier family 6

Gene summary

SLC6A16 shows structural characteristics of an Na(+)- and Cl(-)-dependent neurotransmitter transporter, including 12 transmembrane (TM) domains, intracellular N and C termini, and large extracellular loops containing multiple N-glycosylation sites.[supplied by OMIM, Mar 2008]

MANE transcript

NM_014037.3

Inheritance

—

ClinVar variants

U:105B:15

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.77

Max pathogenic AF

—

Genomic locus

chr19:49,289,638-49,325,215

External References & Databases

Ensembl (ENSG00000063127)

Transcript & Mutation Effects

hg38 • Region Span ~35.6 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 SLC6A16 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 114

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014037.3. 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
missense			101 clinvar	15 clinvar		116
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	105	15	0	120

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014037.3	RefSeq	NP_054756.2	11	MANE Select
ENST00000335875.9	Ensembl	ENSP00000338627.3	11	MANE Select
ENST00000454748.7	Ensembl	ENSP00000404022.2	10	Standard
ENST00000454748.8	Ensembl	ENSP00000404022.2	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Nuclear Receptors Meta-Pathway
NRF2 pathway

Biological Process

neurotransmitter transport
transmembrane transport

Molecular Function

neurotransmitter transporter activity
neurotransmitter:sodium symporter activity

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000335875
Coding exons: 11
Length: 35588
Individuals with no LoFs: 124727
Homozygous LoFs: 0
Heterozygous LoFs: 68
Defined: 124795
p: 0.000272

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.993	360	417	0.863	0.0000225	4815
Missense (PolyPhen)		97	113.73	0.85293		1506
Synonymous	0.694	151	162	0.931	0.00000920	1493
Loss of Function	1.18	23	30.0	0.768	0.00000145	323

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00045	0.00045	rare
Latino/Admixed American	0.00067	0.00067	rare
Ashkenazi Jewish	0.00030	0.00020	rare
East Asian	0.00022	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00024	0.00024	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0649

Intolerance Scores

LoFtool: 0.777
RVIS EVS: -0.6
RVIS percentile EVS: 18.21

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0324

Gene Damage Prediction

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