SLC27A3

solute carrier family 27 member 3, the group of Solute carrier family 27|Acyl-CoA synthetase family

Basic information

Region (hg38): 1:153774354-153780157

Links

ENSG00000143554 ∙ NCBI:11000 ∙ OMIM:604193 ∙ HGNC:10997 ∙ Uniprot:Q5K4L6 ∙ 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 SLC27A3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC27A3 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				2		2
missense			86	3		89
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		2	3
Total	0	0	87	5	2

Variants in SLC27A3

This is a list of pathogenic ClinVar variants found in the SLC27A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153775372-C-T		not specified	Uncertain significance (Aug 13, 2021)
1-153775397-A-C		not specified	Uncertain significance (Dec 21, 2022)
1-153775423-G-A		not specified	Uncertain significance (Mar 18, 2024)
1-153775444-G-A		not specified	Uncertain significance (Nov 11, 2024)
1-153775447-A-T		not specified	Uncertain significance (Apr 22, 2024)
1-153775471-A-C		not specified	Uncertain significance (Dec 13, 2021)
1-153775478-C-G		not specified	Uncertain significance (Aug 13, 2021)
1-153775562-T-G		not specified	Uncertain significance (Aug 06, 2024)
1-153775609-C-A			Likely benign (Sep 01, 2022)
1-153775627-A-G			Likely benign (Dec 01, 2022)
1-153775628-G-A		not specified	Uncertain significance (May 20, 2024)
1-153775667-A-C		not specified	Uncertain significance (Aug 16, 2021)
1-153775685-G-T			not provided (-)
1-153775742-C-G		not specified	Uncertain significance (Jun 07, 2023)
1-153775744-T-A		not specified	Uncertain significance (Oct 19, 2024)
1-153775766-G-T		not specified	Uncertain significance (May 02, 2023)
1-153775780-G-A		not specified	Uncertain significance (Oct 12, 2021)
1-153775789-C-A		not specified	Uncertain significance (Nov 19, 2022)
1-153775810-C-T		not specified	Uncertain significance (Feb 08, 2025)
1-153775849-G-A		not specified	Uncertain significance (Dec 17, 2023)
1-153775856-G-A		not specified	Uncertain significance (Aug 01, 2024)
1-153775865-G-A		not specified	Uncertain significance (Sep 26, 2022)
1-153775877-C-T		not specified	Uncertain significance (Jan 20, 2023)
1-153775934-C-T		not specified	Uncertain significance (Jan 08, 2024)
1-153775951-G-T		not specified	Uncertain significance (Jun 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC27A3	protein_coding	protein_coding	ENST00000368661	10	5804

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.27e-22	0.000383	124968	4	776	125748	0.00311

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.35	485	408	1.19	0.0000233	4544
Missense in Polyphen		205	165.82	1.2363		1813
Synonymous	-2.19	214	177	1.21	0.00000999	1642
Loss of Function	-0.476	31	28.3	1.10	0.00000139	308

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00536	0.00537
Ashkenazi Jewish	0.000597	0.000595
East Asian	0.0149	0.0148
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00180	0.00178
Middle Eastern	0.0149	0.0148
South Asian	0.00444	0.00439
Other	0.00474	0.00473

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has acyl-CoA ligase activity for long-chain and very- long-chain fatty acids. Does not exhibit fatty acid transport activity (By similarity). {ECO:0000250}.
• Pathway: Insulin resistance - Homo sapiens (human);Metabolism of lipids;Fatty acyl-CoA biosynthesis;Metabolism;Fatty acid metabolism;De novo fatty acid biosynthesis;Synthesis of very long-chain fatty acyl-CoAs (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.971
• rvis_EVS: -0.82
• rvis_percentile_EVS: 12.01

Haploinsufficiency Scores

• pHI: 0.0571
• hipred: N
• hipred_score: 0.144
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.161

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc27a3

Gene ontology

• Biological process: long-chain fatty acid metabolic process;long-chain fatty acid transport
• Cellular component: mitochondrion;endoplasmic reticulum;membrane;integral component of membrane;mitochondrial membrane
• Molecular function: nucleotide binding;long-chain fatty acid-CoA ligase activity;long-chain fatty acid transporter activity;very long-chain fatty acid-CoA ligase activity