SLC6A17

solute carrier family 6 member 17, the group of Solute carrier family 6

Basic information

Region (hg38): 1:110150494-110202202

Links

ENSG00000197106

∙ NCBI:388662 ∙ OMIM:610299 ∙ HGNC:31399 ∙ Uniprot:Q9H1V8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown
progressive essential tremor-speech impairment-facial dysmorphism-intellectual disability-abnormal behavior syndrome (Strong), mode of inheritance: AR
progressive essential tremor-speech impairment-facial dysmorphism-intellectual disability-abnormal behavior syndrome (Supportive), mode of inheritance: AR
progressive essential tremor-speech impairment-facial dysmorphism-intellectual disability-abnormal behavior syndrome (Limited), mode of inheritance: AR
progressive essential tremor-speech impairment-facial dysmorphism-intellectual disability-abnormal behavior syndrome (Limited), mode of inheritance: AR
progressive essential tremor-speech impairment-facial dysmorphism-intellectual disability-abnormal behavior syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal recessive 48	AR	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	Craniofacial; Neurologic	25704603

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC6A17 gene.

not_specified (81 variants)
not_provided (25 variants)
Progressive_essential_tremor-speech_impairment-facial_dysmorphism-intellectual_disability-abnormal_behavior_syndrome (18 variants)
SLC6A17-related_disorder (5 variants)
Long_QT_syndrome (1 variants)
See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC6A17 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001010898.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				21 clinvar	2 clinvar	23
missense	2 clinvar		77 clinvar	8 clinvar	1 clinvar	88
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	2	0	78	29	3

Highest pathogenic variant AF is 0.00000410442

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC6A17	protein_coding	protein_coding	ENST00000331565	11	51717

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.504	0.496	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.39	313	456	0.686	0.0000279	4752
Missense in Polyphen		116	192.89	0.60137		2004
Synonymous	1.05	181	200	0.905	0.0000133	1470
Loss of Function	3.86	6	28.0	0.214	0.00000132	321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000705	0.0000703
Middle Eastern	0.000272	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Functions as a sodium-dependent vesicular transporter selective for proline, glycine, leucine and alanine. In contrast to other members of this neurotransmitter transporter family, does not appear to be chloride-dependent (By similarity). {ECO:0000250|UniProtKB:P31662}.;
Disease: DISEASE: Mental retardation, autosomal recessive 48 (MRT48) [MIM:616269]: A form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRT48 patients show moderate to severe intellectual disability and additional features including progressive tremor, speech impairment, and sometimes behavioral problems. {ECO:0000269|PubMed:25704603}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway (Consensus)

Recessive Scores

pRec: 0.113

Intolerance Scores

loftool: 0.244
rvis_EVS: -0.57
rvis_percentile_EVS: 18.9

Haploinsufficiency Scores

pHI: 0.304
hipred: Y
hipred_score: 0.809
ghis: 0.661

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.236

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Slc6a17
Phenotype

Gene ontology

Biological process: brain development;neutral amino acid transport;glycine transport;leucine transport;proline transport;alanine transport;transmembrane transport
Cellular component: integral component of plasma membrane;synaptic vesicle;cell junction;integral component of synaptic vesicle membrane;glutamatergic synapse;GABA-ergic synapse
Molecular function: neurotransmitter:sodium symporter activity