SLC36A1

solute carrier family 36 member 1, the group of Solute carrier family 36

Basic information

Region (hg38): 5:151437046-151492379

Links

ENSG00000123643 ∙ NCBI:206358 ∙ OMIM:606561 ∙ HGNC:18761 ∙ Uniprot:Q7Z2H8 ∙ 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 SLC36A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC36A1 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					1	1
missense			31	3	2	36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	31	3	3

Variants in SLC36A1

This is a list of pathogenic ClinVar variants found in the SLC36A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-151458862-A-T		not specified	Uncertain significance (Jun 29, 2023)
5-151458884-A-G		not specified	Uncertain significance (Jun 26, 2024)
5-151458922-A-C		not specified	Uncertain significance (Sep 07, 2022)
5-151463641-G-T		not specified	Likely benign (Jul 08, 2022)
5-151464526-A-T		not specified	Uncertain significance (Aug 01, 2024)
5-151464556-C-T		not specified	Uncertain significance (Sep 03, 2024)
5-151464599-G-A		not specified	Likely benign (Dec 19, 2023)
5-151465076-T-C		not specified	Uncertain significance (Dec 04, 2024)
5-151465147-C-T		not specified	Uncertain significance (Jun 29, 2023)
5-151465148-G-A		not specified	Uncertain significance (Dec 03, 2021)
5-151467200-C-A		not specified	Uncertain significance (Jul 30, 2024)
5-151467200-C-G		not specified	Uncertain significance (Aug 12, 2021)
5-151467200-C-T			Benign (May 24, 2018)
5-151467227-A-G		not specified	Uncertain significance (Feb 23, 2023)
5-151467262-T-TCTGG		Autism	Uncertain significance (-)
5-151467755-A-G		not specified	Uncertain significance (Aug 01, 2024)
5-151467756-C-T		not specified	Uncertain significance (Jun 11, 2021)
5-151467763-T-G		not specified	Uncertain significance (Feb 16, 2023)
5-151467857-A-G		not specified	Likely benign (Feb 06, 2023)
5-151467882-C-T		not specified	Uncertain significance (Aug 30, 2024)
5-151467909-A-G		not specified	Uncertain significance (Jul 09, 2021)
5-151473691-C-A		not specified	Uncertain significance (Nov 02, 2023)
5-151476642-T-C		not specified	Uncertain significance (Nov 14, 2024)
5-151476672-T-C		not specified	Uncertain significance (May 03, 2023)
5-151476680-A-T		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC36A1	protein_coding	protein_coding	ENST00000243389	10	55336

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000140	0.958	125672	0	76	125748	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.38	220	286	0.770	0.0000164	3099
Missense in Polyphen		49	81.966	0.59781		988
Synonymous	0.0328	123	123	0.996	0.00000764	989
Loss of Function	1.92	13	22.9	0.567	0.00000133	230

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00154	0.00154
Ashkenazi Jewish	0.00	0.00
East Asian	0.000599	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.000599	0.000598
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Neutral amino acid/proton symporter. Has a pH-dependent electrogenic transport activity for small amino acids such as glycine, alanine and proline. Besides small apolar L-amino acids, it also recognizes their D-enantiomers and selected amino acid derivatives such as gamma-aminobutyric acid (By similarity). {ECO:0000250, ECO:0000269|PubMed:12809675}.
• Pathway: Protein digestion and absorption - Homo sapiens (human);Amino acid transport across the plasma membrane;Amino acid and oligopeptide SLC transporters;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Proton-coupled neutral amino acid transporters;Histidine metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Bile acid biosynthesis;Porphyrin metabolism;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.656
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.36

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.359
• ghis: 0.547

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.858

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc36a1

Gene ontology

• Biological process: amino acid transmembrane transport;ion transport;amino acid transport;L-alanine transport;glycine transport;proline transmembrane transport;proton transmembrane transport
• Cellular component: lysosomal membrane;endoplasmic reticulum;plasma membrane;integral component of membrane
• Molecular function: amino acid:proton symporter activity;proton transmembrane transporter activity;amino acid transmembrane transporter activity;L-alanine transmembrane transporter activity;glycine transmembrane transporter activity;L-proline transmembrane transporter activity