SLC27A5

solute carrier family 27 member 5, the group of Solute carrier family 27|Acyl-CoA synthetase family

Basic information

Region (hg38): 19:58479512-58512413

Links

ENSG00000083807 ∙ NCBI:10998 ∙ OMIM:603314 ∙ HGNC:10999 ∙ Uniprot:Q9Y2P5 ∙ 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 SLC27A5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC27A5 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			14	22	4	40
missense			111	9	3	123
nonsense						0
start loss			1			1
frameshift			4			4
inframe indel			3			3
splice donor/acceptor (+/-2bp)			1			1
splice region				3	1	4
non coding			5	3	4	12
Total	0	0	139	34	11

Variants in SLC27A5

This is a list of pathogenic ClinVar variants found in the SLC27A5 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-58479665-G-A		not specified	Uncertain significance (Nov 04, 2022)
19-58479682-T-C		not specified	Uncertain significance (May 21, 2024)
19-58479936-C-T		not specified	Uncertain significance (Dec 20, 2023)
19-58479998-G-A		not specified	Uncertain significance (Sep 03, 2024)
19-58480005-G-A		not specified	Uncertain significance (Sep 23, 2023)
19-58480017-C-G		not specified	Uncertain significance (Jul 22, 2024)
19-58480176-G-T		not specified	Uncertain significance (Dec 02, 2024)
19-58480226-G-T		Short stature	Uncertain significance (Nov 18, 2001)
19-58480268-A-G		not specified	Uncertain significance (Nov 12, 2021)
19-58480278-C-A		not specified	Uncertain significance (Dec 11, 2023)
19-58480286-C-A		not specified	Uncertain significance (Sep 04, 2024)
19-58480343-C-A		not specified	Uncertain significance (Sep 23, 2023)
19-58480356-C-T			Likely benign (Jan 01, 2023)
19-58480389-G-A		not specified	Uncertain significance (Aug 14, 2023)
19-58480391-G-A		not specified	Uncertain significance (Apr 08, 2022)
19-58480391-G-C		not specified	Uncertain significance (Feb 23, 2023)
19-58480392-G-C		not specified	Uncertain significance (Aug 17, 2022)
19-58480401-G-A		Short stature	Pathogenic (Nov 18, 2001)
19-58480428-G-A		not specified	Uncertain significance (Jan 23, 2023)
19-58480428-G-T		not specified	Uncertain significance (Oct 18, 2021)
19-58480434-A-G		not specified	Uncertain significance (Nov 09, 2022)
19-58480437-C-T		not specified	Uncertain significance (Aug 03, 2022)
19-58480464-G-A		not specified	Uncertain significance (Feb 28, 2024)
19-58480475-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
19-58480524-A-G		not specified	Uncertain significance (Aug 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC27A5	protein_coding	protein_coding	ENST00000263093	10	32902

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.37e-15	0.0664	125582	0	166	125748	0.000660

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.399	401	424	0.946	0.0000258	4322
Missense in Polyphen		118	141.68	0.83288		1609
Synonymous	1.43	160	185	0.866	0.0000109	1539
Loss of Function	0.694	24	28.0	0.858	0.00000144	281

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00169	0.00157
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000558	0.000544
Finnish	0.00135	0.00134
European (Non-Finnish)	0.000600	0.000589
Middle Eastern	0.000558	0.000544
South Asian	0.000760	0.000686
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acyl-CoA synthetase involved in bile acid metabolism. Proposed to catalyze the first step in the conjugation of C24 bile acids (choloneates) to glycine and taurine before excretion into bile canaliculi by activating them to their CoA thioesters. Seems to activate secondary bile acids entering the liver from the enterohepatic circulation. In vitro, also 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. {ECO:0000269|PubMed:10749848, ECO:0000269|PubMed:11980911}.
• Pathway: Insulin resistance - Homo sapiens (human);Bile secretion - Homo sapiens (human);Primary bile acid biosynthesis - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);27-Hydroxylase Deficiency;Bile Acid Biosynthesis;Congenital Bile Acid Synthesis Defect Type II;Cerebrotendinous Xanthomatosis (CTX);Zellweger Syndrome;Familial Hypercholanemia (FHCA);Congenital Bile Acid Synthesis Defect Type III;Farnesoid X Receptor Pathway;Nuclear Receptors Meta-Pathway;PPAR signaling pathway;Metabolism of lipids;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;Recycling of bile acids and salts;Bile acid and bile salt metabolism;Metabolism of steroids;Bile acid biosynthesis;bile acid biosynthesis, neutral pathway;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.150

Intolerance Scores

• loftool: 0.851
• rvis_EVS: 0.29
• rvis_percentile_EVS: 71.6

Haploinsufficiency Scores

• pHI: 0.0742
• hipred: N
• hipred_score: 0.146
• ghis: 0.460

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.810

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc27a5
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype

Gene ontology

• Biological process: very long-chain fatty acid metabolic process;long-chain fatty acid metabolic process;triglyceride mobilization;bile acid biosynthetic process;bile acid metabolic process;bile acid and bile salt transport;plasma membrane long-chain fatty acid transport;ketone body biosynthetic process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;basal plasma membrane;integral component of endoplasmic reticulum membrane;protein-containing complex
• Molecular function: long-chain fatty acid-CoA ligase activity;long-chain fatty acid transporter activity;ATP binding;fatty acid transmembrane transporter activity;very long-chain fatty acid-CoA ligase activity;protein-containing complex binding;cholate-CoA ligase activity