RETSAT

retinol saturase

Basic information

Region (hg38): 2:85341954-85354531

Links

ENSG00000042445 ∙ NCBI:54884 ∙ OMIM:617597 ∙ HGNC:25991 ∙ Uniprot:Q6NUM9 ∙ 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 RETSAT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RETSAT 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					4	4
missense			45	2	1	48
nonsense						0
start loss						0
frameshift				1	1	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	3	6

Variants in RETSAT

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

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

Position	Type	Phenotype	Significance	ClinVar
2-85343258-T-G		not specified	Uncertain significance (Oct 26, 2022)
2-85343262-C-T		not specified	Uncertain significance (Jan 08, 2024)
2-85343265-G-A		not specified	Uncertain significance (Apr 26, 2023)
2-85343265-G-T			Benign (Jul 12, 2018)
2-85343307-G-A		not specified	Uncertain significance (Sep 17, 2021)
2-85343343-G-T		not specified	Uncertain significance (Jun 02, 2024)
2-85343355-C-G		not specified	Uncertain significance (Jun 02, 2023)
2-85343375-T-C		not specified	Uncertain significance (Apr 25, 2023)
2-85343376-C-A		not specified	Uncertain significance (Feb 14, 2023)
2-85343657-G-T		not specified	Uncertain significance (Jan 03, 2022)
2-85343674-C-T		not specified	Uncertain significance (Jan 03, 2022)
2-85343699-G-A		not specified	Uncertain significance (Jun 01, 2023)
2-85343704-C-T		not specified	Uncertain significance (Jan 18, 2023)
2-85343770-A-G		not specified	Uncertain significance (Aug 17, 2021)
2-85344042-G-A		not specified	Uncertain significance (Dec 15, 2023)
2-85344072-TCA-T			Benign (Jul 12, 2018)
2-85344087-C-T		not specified	Uncertain significance (Feb 23, 2023)
2-85344118-C-G		not specified	Uncertain significance (Oct 05, 2023)
2-85344243-G-T		not specified	Uncertain significance (Feb 16, 2023)
2-85344262-G-A		not specified	Uncertain significance (Aug 10, 2021)
2-85344281-A-G		not specified	Uncertain significance (Dec 18, 2023)
2-85344309-C-T			Benign (Jun 12, 2018)
2-85344310-G-A			Benign (Jul 12, 2018)
2-85344663-C-T		not specified	Uncertain significance (Jul 14, 2021)
2-85344666-C-T		not specified	Likely benign (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RETSAT	protein_coding	protein_coding	ENST00000295802	11	12533

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.83e-14	0.213	122995	29	2724	125748	0.0110

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.113	342	348	0.983	0.0000191	3914
Missense in Polyphen		73	80.514	0.90668		920
Synonymous	-0.150	147	145	1.02	0.00000796	1279
Loss of Function	1.08	24	30.5	0.788	0.00000191	302

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0295	0.0293
Ashkenazi Jewish	0.00288	0.00288
East Asian	0.0952	0.0593
Finnish	0.0118	0.0118
European (Non-Finnish)	0.00459	0.00455
Middle Eastern	0.0952	0.0593
South Asian	0.00644	0.00554
Other	0.0113	0.00933

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the saturation of all-trans-retinol to all- trans-13,14-dihydroretinol. Does not exhibit any activity toward all-trans-retinoic acid, nor 9-cis, 11-cis or 13-cis-retinol isomers. May play a role in the metabolism of vitamin A. Independently of retinol conversion, may regulate liver metabolism upstream of MLXIPL/ChREBP. May play a role in adipocyte differentiation. {ECO:0000250|UniProtKB:Q64FW2}.
• Pathway: Retinol metabolism - Homo sapiens (human);Vitamin A Deficiency;Retinol Metabolism;Vitamin A and Carotenoid Metabolism;Signaling by GPCR;Signal Transduction;Metabolism of fat-soluble vitamins;Metabolism;Metabolism of vitamins and cofactors;Retinoid metabolism and transport;G alpha (i) signalling events;Visual phototransduction;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.0935

Intolerance Scores

• loftool: 0.956
• rvis_EVS: 0.07
• rvis_percentile_EVS: 59.16

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.197
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.462

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Retsat
• Phenotype: hematopoietic system phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: retinol metabolic process;oxidation-reduction process
• Cellular component: nuclear outer membrane;endoplasmic reticulum membrane;membrane;nuclear membrane
• Molecular function: oxidoreductase activity;all-trans-retinol 13,14-reductase activity