SLC27A2

solute carrier family 27 member 2, the group of Acyl-CoA synthetase family|Solute carrier family 27

Basic information

Region (hg38): 15:50182195-50236385

Previous symbols: [ "FACVL1" ]

Links

ENSG00000140284 ∙ NCBI:11001 ∙ OMIM:603247 ∙ HGNC:10996 ∙ Uniprot:O14975 ∙ 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 SLC27A2 gene.

• Inborn genetic diseases (28 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC27A2 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			27	1		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	2	0

Variants in SLC27A2

This is a list of pathogenic ClinVar variants found in the SLC27A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-50182579-C-T		not specified	Uncertain significance (Mar 28, 2023)
15-50182604-C-G		not specified	Uncertain significance (Dec 06, 2022)
15-50182690-G-A		not specified	Uncertain significance (Sep 22, 2021)
15-50182707-G-A		not specified	Uncertain significance (Feb 15, 2023)
15-50182722-C-G		not specified	Uncertain significance (Mar 30, 2022)
15-50182759-T-G		not specified	Uncertain significance (Mar 01, 2024)
15-50182784-G-T		not specified	Uncertain significance (Apr 05, 2023)
15-50182837-A-G		not specified	Uncertain significance (Mar 08, 2024)
15-50182872-T-A		not specified	Uncertain significance (Feb 15, 2023)
15-50182878-G-C		not specified	Uncertain significance (Dec 21, 2023)
15-50197602-T-C		not specified	Uncertain significance (Jan 31, 2023)
15-50197634-C-G		not specified	Uncertain significance (Oct 04, 2022)
15-50202504-A-G		not specified	Likely benign (Apr 29, 2022)
15-50202526-G-T		not specified	Uncertain significance (Aug 08, 2023)
15-50202544-C-T		not specified	Uncertain significance (Aug 23, 2021)
15-50202555-G-A		not specified	Uncertain significance (Jul 13, 2021)
15-50202606-G-A		not specified	Uncertain significance (Aug 22, 2023)
15-50202636-A-G		not specified	Uncertain significance (Nov 01, 2022)
15-50202637-T-C		not specified	Uncertain significance (Mar 20, 2023)
15-50205256-C-T		not specified	Uncertain significance (May 18, 2023)
15-50205321-G-T		not specified	Uncertain significance (May 09, 2023)
15-50223116-C-T		not specified	Uncertain significance (Apr 22, 2022)
15-50223117-G-A		not specified	Likely benign (Jan 03, 2024)
15-50223131-C-T		not specified	Uncertain significance (Sep 07, 2022)
15-50226030-G-A		not specified	Uncertain significance (Jul 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC27A2	protein_coding	protein_coding	ENST00000267842	10	54200

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.36e-9	0.872	125652	0	96	125748	0.000382

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.191	359	349	1.03	0.0000174	4015
Missense in Polyphen		118	123.41	0.95613		1426
Synonymous	0.206	132	135	0.977	0.00000661	1236
Loss of Function	1.70	17	26.4	0.644	0.00000121	335

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00203	0.00203
Ashkenazi Jewish	0.00	0.00
East Asian	0.000823	0.000816
Finnish	0.000144	0.000139
European (Non-Finnish)	0.000274	0.000273
Middle Eastern	0.000823	0.000816
South Asian	0.000132	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acyl-CoA synthetase probably involved in bile acid metabolism. Proposed to activate C27 precursors of bile acids to their CoA thioesters derivatives before side chain cleavage via peroxisomal beta-oxidation occurs. In vitro, activates 3-alpha,7- alpha,12-alpha-trihydroxy-5-beta-cholestanate (THCA), the C27 precursor of cholic acid deriving from the de novo synthesis from cholesterol. Does not utilize C24 bile acids as substrates. In vitro, also activates long- and branched-chain fatty acids and may have additional roles in fatty acid metabolism. May be involved in translocation of long-chain fatty acids (LFCA) across membranes (By similarity). {ECO:0000250, ECO:0000269|PubMed:11980911}.
• Pathway: Insulin resistance - Homo sapiens (human);Peroxisome - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);Metformin Pathway, Pharmacokinetics;Refsum Disease;Phytanic Acid Peroxisomal Oxidation;PPAR signaling pathway;stearate biosynthesis;Neutrophil degranulation;Metabolism of lipids;fatty acid activation;Metabolism of proteins;Alpha-oxidation of phytanate;Leukotriene metabolism;Omega-3 fatty acid metabolism;Peroxisomal lipid metabolism;Innate Immune System;Immune System;Metabolism;Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol;Synthesis of bile acids and bile salts via 24-hydroxycholesterol;Synthesis of bile acids and bile salts;Bile acid and bile salt metabolism;Peroxisomal protein import;Fatty acid metabolism;Metabolism of steroids;γ-linolenate biosynthesis;Mono-unsaturated fatty acid beta-oxidation;Omega-6 fatty acid metabolism;Bile acid biosynthesis;Di-unsaturated fatty acid beta-oxidation;Phytanic acid peroxisomal oxidation;fatty acid β-oxidation (peroxisome);fatty acid α-oxidation;fatty acid β-oxidation;bile acid biosynthesis, neutral pathway (Consensus)

Recessive Scores

• pRec: 0.181

Intolerance Scores

• loftool: 0.877
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.65

Haploinsufficiency Scores

• pHI: 0.474
• hipred: N
• hipred_score: 0.281
• ghis: 0.477

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.934

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc27a2
• Phenotype: cellular phenotype; normal phenotype

Gene ontology

• Biological process: fatty acid alpha-oxidation;long-chain fatty acid metabolic process;protein targeting to peroxisome;fatty acid beta-oxidation;bile acid biosynthetic process;very long-chain fatty acid catabolic process;neutrophil degranulation;long-chain fatty acid import;methyl-branched fatty acid metabolic process
• Cellular component: peroxisomal membrane;integral component of peroxisomal membrane;endoplasmic reticulum;endoplasmic reticulum lumen;endoplasmic reticulum membrane;cytosol;plasma membrane;integral component of endoplasmic reticulum membrane;specific granule membrane;extracellular exosome
• Molecular function: long-chain fatty acid-CoA ligase activity;signaling receptor binding;long-chain fatty acid transporter activity;ATP binding;fatty acid transmembrane transporter activity;enzyme binding;very long-chain fatty acid-CoA ligase activity;phytanate-CoA ligase activity;pristanate-CoA ligase activity;decanoate-CoA ligase activity