SLC6A16

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

Basic information

Region (hg38): 19:49289638-49325215

Links

ENSG00000063127 ∙ NCBI:28968 ∙ OMIM:607972 ∙ HGNC:13622 ∙ Uniprot:Q9GZN6 ∙ 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 SLC6A16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC6A16 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			36	6		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	6	0

Variants in SLC6A16

This is a list of pathogenic ClinVar variants found in the SLC6A16 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-49290243-C-T		not specified	Likely benign (Nov 22, 2022)
19-49290244-A-C		not specified	Uncertain significance (Apr 15, 2024)
19-49290257-C-T		not specified	Likely benign (Jul 25, 2023)
19-49290261-C-G		not specified	Uncertain significance (Sep 12, 2023)
19-49290272-A-G		not specified	Uncertain significance (Aug 26, 2022)
19-49290289-C-T		not specified	Uncertain significance (Jul 10, 2024)
19-49290290-G-A		not specified	Uncertain significance (Dec 08, 2023)
19-49290338-G-T		not specified	Uncertain significance (Feb 02, 2022)
19-49290364-G-A		not specified	Uncertain significance (Dec 06, 2024)
19-49290376-C-T		not specified	Uncertain significance (Mar 12, 2024)
19-49290750-G-T		not specified	Uncertain significance (Nov 09, 2024)
19-49293266-C-T		not specified	Likely benign (May 30, 2024)
19-49293319-A-G		not specified	Uncertain significance (Dec 05, 2022)
19-49293331-G-A		not specified	Uncertain significance (Jun 18, 2024)
19-49293350-G-T		not specified	Uncertain significance (Apr 22, 2024)
19-49293841-G-C		not specified	Uncertain significance (Sep 02, 2024)
19-49293889-C-A		not specified	Uncertain significance (Dec 06, 2021)
19-49293895-A-G		not specified	Uncertain significance (Dec 07, 2021)
19-49293977-A-G		not specified	Uncertain significance (Dec 19, 2022)
19-49294019-C-T		not specified	Uncertain significance (Oct 06, 2021)
19-49294408-G-A		not specified	Uncertain significance (Oct 06, 2021)
19-49294429-G-A		not specified	Uncertain significance (Aug 27, 2024)
19-49294455-T-C		not specified	Uncertain significance (Feb 12, 2024)
19-49294456-T-C		not specified	Uncertain significance (Dec 18, 2023)
19-49294512-A-G		not specified	Uncertain significance (Nov 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC6A16	protein_coding	protein_coding	ENST00000335875	11	35588

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.29e-13	0.310	124727	0	68	124795	0.000272

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.993	360	417	0.863	0.0000225	4815
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00112	0.00112
Ashkenazi Jewish	0.000304	0.000199
East Asian	0.000223	0.000223
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000239	0.000238
Middle Eastern	0.000223	0.000223
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway (Consensus)

Recessive Scores

• pRec: 0.0649

Intolerance Scores

• loftool: 0.777
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.21

Haploinsufficiency Scores

• pHI: 0.0620
• hipred: N
• hipred_score: 0.123
• ghis: 0.438

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0324

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc6a16

Gene ontology

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