SLC6A17

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

Basic information

Region (hg38): 1:110150493-110202202

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 provided (21 variants)
• Inborn genetic diseases (16 variants)
• Progressive essential tremor-speech impairment-facial dysmorphism-intellectual disability-abnormal behavior syndrome (16 variants)
• not specified (15 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.

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				15	4	19
missense			24	2	2	28
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	1		2
non coding					1	1
Total	0	0	25	17	7

Variants in SLC6A17

This is a list of pathogenic ClinVar variants found in the SLC6A17 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-110166958-G-A		Progressive essential tremor-speech impairment-facial dysmorphism-intellectual disability-abnormal behavior syndrome	Uncertain significance (Nov 30, 2018)
1-110167010-C-G			Benign (Jun 01, 2018)
1-110167093-T-C		not specified	Uncertain significance (Feb 06, 2023)
1-110167097-T-C		Progressive essential tremor-speech impairment-facial dysmorphism-intellectual disability-abnormal behavior syndrome	Benign (Jul 15, 2021)
1-110167098-G-A		Progressive essential tremor-speech impairment-facial dysmorphism-intellectual disability-abnormal behavior syndrome	Benign (Jul 15, 2021)
1-110167104-G-A		not specified	Uncertain significance (May 18, 2022)
1-110167137-A-G		not specified	Uncertain significance (Jan 04, 2024)
1-110167150-T-C		not specified	Uncertain significance (May 05, 2023)
1-110167225-A-G		Progressive essential tremor-speech impairment-facial dysmorphism-intellectual disability-abnormal behavior syndrome • not specified	Conflicting classifications of pathogenicity (May 30, 2018)
1-110172076-C-A		not specified	Likely benign (May 17, 2016)
1-110172100-C-T			Likely benign (Jun 13, 2018)
1-110172124-G-T		Progressive essential tremor-speech impairment-facial dysmorphism-intellectual disability-abnormal behavior syndrome	Uncertain significance (Aug 30, 2022)
1-110172144-T-C		not specified	Uncertain significance (Jan 03, 2022)
1-110172147-G-A		Progressive essential tremor-speech impairment-facial dysmorphism-intellectual disability-abnormal behavior syndrome	Uncertain significance (Aug 30, 2022)
1-110172187-C-A			Likely benign (May 01, 2023)
1-110172197-A-G			Likely benign (Dec 31, 2019)
1-110174012-G-A		Progressive essential tremor-speech impairment-facial dysmorphism-intellectual disability-abnormal behavior syndrome	Pathogenic (Mar 05, 2015)
1-110174017-G-C		not specified	Uncertain significance (Apr 14, 2017)
1-110174053-G-A		not specified • Progressive essential tremor-speech impairment-facial dysmorphism-intellectual disability-abnormal behavior syndrome	Benign/Likely benign (Apr 11, 2023)
1-110174076-T-C		not specified	Uncertain significance (Jan 23, 2024)
1-110174879-C-T			Likely benign (Jun 12, 2018)
1-110174903-C-T		not specified	Likely benign (Aug 03, 2017)
1-110174904-G-A			Benign (Dec 31, 2019)
1-110174933-C-T			Likely benign (Aug 22, 2018)
1-110174934-G-A		not specified	Uncertain significance (Sep 20, 2023)

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

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