SLC36A4

solute carrier family 36 member 4, the group of Solute carrier family 36

Basic information

Region (hg38): 11:93144173-93197991

Links

ENSG00000180773 ∙ NCBI:120103 ∙ OMIM:613760 ∙ HGNC:19660 ∙ Uniprot:Q6YBV0 ∙ 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 SLC36A4 gene.

• Inborn genetic diseases (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC36A4 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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in SLC36A4

This is a list of pathogenic ClinVar variants found in the SLC36A4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-93148580-A-G		not specified	Likely benign (Feb 07, 2023)
11-93148617-T-C		not specified	Uncertain significance (Sep 01, 2021)
11-93148700-A-T		not specified	Uncertain significance (Oct 05, 2023)
11-93148730-G-A		not specified	Uncertain significance (Jan 19, 2024)
11-93148820-C-T		not specified	Uncertain significance (Jun 11, 2021)
11-93148829-A-T		not specified	Uncertain significance (Feb 28, 2024)
11-93148839-C-T		not specified	Uncertain significance (Feb 27, 2023)
11-93154255-G-C		not specified	Uncertain significance (Mar 28, 2023)
11-93162716-G-C		not specified	Uncertain significance (Dec 15, 2023)
11-93162757-A-C		not specified	Uncertain significance (Dec 06, 2022)
11-93162775-G-A		not specified	Uncertain significance (Oct 12, 2022)
11-93165935-A-T		not specified	Uncertain significance (Apr 12, 2023)
11-93167945-C-A		not specified	Uncertain significance (Nov 17, 2022)
11-93168022-C-A		not specified	Uncertain significance (Mar 11, 2022)
11-93168032-C-G		not specified	Uncertain significance (Aug 16, 2022)
11-93168060-G-A		not specified	Uncertain significance (Nov 21, 2023)
11-93168101-C-T		not specified	Uncertain significance (May 25, 2022)
11-93168122-T-C		not specified	Uncertain significance (Feb 28, 2023)
11-93180825-A-G		not specified	Uncertain significance (Nov 08, 2022)
11-93180831-A-G		not specified	Uncertain significance (May 24, 2023)
11-93180859-C-T		not specified	Uncertain significance (Dec 19, 2023)
11-93181716-G-A		not specified	Uncertain significance (Nov 16, 2021)
11-93181731-T-C		not specified	Uncertain significance (Dec 12, 2023)
11-93182831-G-A		not specified	Uncertain significance (May 31, 2023)
11-93182849-A-G		not specified	Uncertain significance (Nov 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC36A4	protein_coding	protein_coding	ENST00000326402	11	53790

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.81e-17	0.00183	125628	0	111	125739	0.000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0410	261	259	1.01	0.0000124	3281
Missense in Polyphen		73	73.158	0.99785		971
Synonymous	0.502	83	89.0	0.932	0.00000420	962
Loss of Function	-0.574	24	21.2	1.13	9.78e-7	292

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000290	0.000289
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000116	0.000109
Finnish	0.00222	0.00222
European (Non-Finnish)	0.000338	0.000334
Middle Eastern	0.000116	0.000109
South Asian	0.000439	0.000425
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a sodium-independent electroneutral transporter for tryptophan, proline and alanine. Inhibited by sarcosine. {ECO:0000269|PubMed:21097500}.
• Pathway: Tryptophan catabolism;Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism;Metabolism of amino acids and derivatives;Metabolism;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 (Consensus)

Intolerance Scores

• loftool: 0.932
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.49

Haploinsufficiency Scores

• pHI: 0.250
• hipred: N
• hipred_score: 0.197
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.479

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc36a4

Gene ontology

• Biological process: amino acid transmembrane transport;L-alanine transport;proline transport;tryptophan transport;L-proline import across plasma membrane;L-tryptophan transmembrane transport
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: amino acid transmembrane transporter activity;L-alanine transmembrane transporter activity;L-proline transmembrane transporter activity;L-tryptophan transmembrane transporter activity;symporter activity