SLC27A4

solute carrier family 27 member 4, the group of Acyl-CoA synthetase family|Solute carrier family 27

Basic information

Region (hg38): 9:128340526-128361470

Links

ENSG00000167114 ∙ NCBI:10999 ∙ OMIM:604194 ∙ HGNC:10998 ∙ Uniprot:Q6P1M0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• ichthyosis prematurity syndrome (Definitive), mode of inheritance: AR
• ichthyosis prematurity syndrome (Strong), mode of inheritance: AR
• ichthyosis prematurity syndrome (Strong), mode of inheritance: AR
• ichthyosis prematurity syndrome (Strong), mode of inheritance: AR
• ichthyosis prematurity syndrome (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ichthyosis prematurity syndrome	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic; Obstetric	19631310; 21856041; 22927265
The obstetric manifestations involve maternal mid-trimester complications of pregnancy leading to prematurity

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC27A4 gene.

• not provided (140 variants)
• Inborn genetic diseases (27 variants)
• Ichthyosis prematurity syndrome (9 variants)
• Lamellar ichthyosis (4 variants)
• not specified (2 variants)
• Autosomal recessive congenital ichthyosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC27A4 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				41	3	44
missense	2	3	41	7	3	56
nonsense	4	2				6
start loss	1					1
frameshift	5	1	1			7
inframe indel				1		1
splice donor/acceptor (+/-2bp)	1	7				8
splice region			1	6	2	9
non coding				18	5	23
Total	13	13	42	67	11

Highest pathogenic variant AF is 0.0000854

Variants in SLC27A4

This is a list of pathogenic ClinVar variants found in the SLC27A4 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-128343125-A-G		Lamellar ichthyosis	Likely pathogenic (May 26, 2022)
9-128343133-A-G			Pathogenic (Aug 24, 2023)
9-128343145-G-T			not provided (-)
9-128343153-G-T			Likely benign (Jul 09, 2023)
9-128343155-TG-T			Pathogenic (Apr 12, 2023)
9-128343159-G-A			Likely benign (Nov 21, 2023)
9-128343160-G-T		Inborn genetic diseases	Uncertain significance (Oct 13, 2023)
9-128343168-G-C			Likely benign (Nov 15, 2023)
9-128343176-A-G			Uncertain significance (Sep 19, 2022)
9-128343178-C-T			Likely benign (Dec 13, 2023)
9-128343195-C-T			Likely benign (Mar 04, 2023)
9-128343203-A-G		Inborn genetic diseases	Uncertain significance (Aug 08, 2022)
9-128343213-C-T			Likely benign (Dec 14, 2023)
9-128343231-C-T			Likely benign (Sep 29, 2023)
9-128343242-G-C		Inborn genetic diseases	Uncertain significance (Aug 22, 2023)
9-128343243-C-T			Likely benign (Sep 20, 2023)
9-128343246-C-T			Likely benign (Nov 05, 2023)
9-128343250-C-T		Inborn genetic diseases	Uncertain significance (Nov 01, 2022)
9-128343260-G-A		Inborn genetic diseases	Uncertain significance (Oct 05, 2022)
9-128343276-C-T			Likely benign (Dec 09, 2023)
9-128343284-G-A			Uncertain significance (Jun 23, 2022)
9-128343285-C-T			Likely benign (Jan 18, 2024)
9-128343291-C-T			Likely benign (Jan 28, 2023)
9-128343307-C-T			Likely benign (Apr 25, 2023)
9-128343308-C-T			Likely benign (May 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC27A4	protein_coding	protein_coding	ENST00000300456	12	20825

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000449	0.998	125670	0	78	125748	0.000310

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.232	400	413	0.968	0.0000299	4142
Missense in Polyphen		158	176.13	0.89707		1760
Synonymous	-0.790	190	177	1.08	0.0000124	1347
Loss of Function	2.76	12	27.7	0.433	0.00000138	316

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000207	0.000206
Ashkenazi Jewish	0.00	0.00
East Asian	0.000222	0.000217
Finnish	0.000633	0.000601
European (Non-Finnish)	0.000449	0.000440
Middle Eastern	0.000222	0.000217
South Asian	0.0000980	0.0000980
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in translocation of long-chain fatty acids (LFCA) across the plasma membrane. Appears to be the principal fatty acid transporter in small intestinal enterocytes. Plays a role in the formation of the epidermal barrier. Required for fat absorption in early embryogenesis. Has acyl-CoA ligase activity for long-chain and very-long-chain fatty acids (VLCFAs). Indirectly inhibits RPE65 via substrate competition and via production of VLCFA derivatives like lignoceroyl-CoA. Prevents light-induced degeneration of rods and cones (By similarity). {ECO:0000250}.
• Pathway: Insulin resistance - Homo sapiens (human);Fat digestion and absorption - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);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: 0.187

Intolerance Scores

• loftool: 0.636
• rvis_EVS: -1.08
• rvis_percentile_EVS: 7.2

Haploinsufficiency Scores

• pHI: 0.128
• hipred: Y
• hipred_score: 0.510
• ghis: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.976

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc27a4
• Phenotype: digestive/alimentary phenotype; skeleton phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; craniofacial phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: medium-chain fatty acid transport;long-chain fatty acid metabolic process;lipid metabolic process;response to nutrient;fatty acid transport;long-chain fatty acid transport;very long-chain fatty acid catabolic process;skin development;long-chain fatty acid import
• Cellular component: endoplasmic reticulum membrane;plasma membrane;microvillus;membrane;integral component of membrane;brush border membrane
• Molecular function: nucleotide binding;long-chain fatty acid-CoA ligase activity;long-chain fatty acid transporter activity;fatty acid transmembrane transporter activity;very long-chain fatty acid-CoA ligase activity