SLC27A1

solute carrier family 27 member 1, the group of Solute carrier family 27|Acyl-CoA synthetase family

Basic information

Region (hg38): 19:17468769-17506168

Links

ENSG00000130304 ∙ NCBI:376497 ∙ OMIM:600691 ∙ HGNC:10995 ∙ Uniprot:Q6PCB7 ∙ 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 SLC27A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC27A1 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					3	3
missense			30	2	1	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	30	2	4

Variants in SLC27A1

This is a list of pathogenic ClinVar variants found in the SLC27A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-17486574-T-C		not specified	Uncertain significance (Mar 24, 2023)
19-17486613-G-T		not specified	Uncertain significance (Jan 19, 2024)
19-17486636-A-G		not specified	Uncertain significance (Dec 27, 2023)
19-17486775-C-G		not specified	Uncertain significance (Apr 20, 2024)
19-17486780-G-A		not specified	Uncertain significance (Jun 04, 2024)
19-17486807-C-T		not specified	Uncertain significance (Dec 20, 2023)
19-17486848-G-A			Benign (Nov 09, 2018)
19-17486854-G-A		not specified	Uncertain significance (Jan 09, 2024)
19-17486882-C-T		not specified	Uncertain significance (Nov 09, 2022)
19-17487211-G-C		not specified	Uncertain significance (Dec 09, 2023)
19-17487224-T-C		not specified	Uncertain significance (Jan 16, 2024)
19-17487254-C-T		not specified	Uncertain significance (May 15, 2023)
19-17487313-G-A			Benign (Dec 31, 2019)
19-17487329-A-C		not specified	Uncertain significance (Jun 16, 2024)
19-17487463-G-A		not specified	Uncertain significance (Jun 11, 2024)
19-17487516-G-A		not specified	Uncertain significance (Sep 26, 2023)
19-17487537-G-A			Benign (Dec 14, 2017)
19-17488892-A-G		not specified	Likely benign (Jun 13, 2023)
19-17489002-C-A			Benign (Jun 11, 2018)
19-17489017-T-A		not specified	Uncertain significance (May 10, 2024)
19-17489088-T-C		not specified	Uncertain significance (Apr 27, 2022)
19-17489115-A-G		not specified	Uncertain significance (Mar 19, 2024)
19-17497258-G-A		not specified	Uncertain significance (May 27, 2022)
19-17497309-G-A		not specified	Uncertain significance (May 28, 2024)
19-17497313-C-T		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC27A1	protein_coding	protein_coding	ENST00000252595	12	37400

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.58e-16	0.0321	125680	0	68	125748	0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.560	406	439	0.925	0.0000302	4080
Missense in Polyphen		107	128.15	0.83498		1182
Synonymous	0.749	186	199	0.933	0.0000148	1366
Loss of Function	0.582	26	29.4	0.884	0.00000159	299

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000872	0.000848
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000267	0.000264
Middle Eastern	0.000272	0.000272
South Asian	0.000264	0.000261
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates the ATP-dependent import of long-chain fatty acids (LCFA) into the cell by mediating their translocation at the plasma membrane (PubMed:28178239). Has also an acyl-CoA ligase activity for long-chain and very-long-chain fatty acids. May act directly as a bona fide transporter, or alternatively, in a cytoplasmic or membrane-associated multimeric protein complex to trap and draw fatty acids towards accumulation. Plays a pivotal role in regulating available LCFA substrates from exogenous sources in tissues undergoing high levels of beta-oxidation or triglyceride synthesis. May be involved in regulation of cholesterol metabolism (By similarity). {ECO:0000250|UniProtKB:Q60714, ECO:0000269|PubMed:28178239}.
• Pathway: Insulin resistance - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);Metformin Pathway, Pharmacokinetics;Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);PPAR Alpha Pathway;Nuclear Receptors Meta-Pathway;PPAR signaling pathway;Transport of fatty acids;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules;De novo fatty acid biosynthesis (Consensus)

Recessive Scores

• pRec: 0.250

Intolerance Scores

• loftool: 0.667
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.46

Haploinsufficiency Scores

• pHI: 0.0901
• hipred: Y
• hipred_score: 0.520
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.777

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc27a1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype

Gene ontology

• Biological process: medium-chain fatty acid transport;long-chain fatty acid metabolic process;phosphatidylethanolamine biosynthetic process;phosphatidic acid biosynthetic process;phosphatidylglycerol biosynthetic process;phosphatidylcholine biosynthetic process;phosphatidylserine biosynthetic process;phosphatidylinositol biosynthetic process;response to cold;positive regulation of triglyceride biosynthetic process;long-chain fatty acid transport;regulation of lipid metabolic process;positive regulation of heat generation;cardiolipin biosynthetic process;response to insulin;adiponectin-activated signaling pathway;long-chain fatty acid import;negative regulation of phospholipid biosynthetic process;positive regulation of protein serine/threonine kinase activity
• Cellular component: mitochondrion;mitochondrial inner membrane;endoplasmic reticulum;cytosol;plasma membrane;integral component of plasma membrane;membrane
• Molecular function: nucleotide binding;long-chain fatty acid-CoA ligase activity;long-chain fatty acid transporter activity;protein binding;fatty acid transmembrane transporter activity;very long-chain fatty acid-CoA ligase activity;protein homodimerization activity