RDH16

retinol dehydrogenase 16, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 12:56951431-56959374

Links

ENSG00000139547 ∙ NCBI:8608 ∙ OMIM:620043 ∙ HGNC:29674 ∙ Uniprot:O75452 ∙ 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 RDH16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RDH16 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						0
missense			26	3	1	30
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	3	2

Variants in RDH16

This is a list of pathogenic ClinVar variants found in the RDH16 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-56952144-C-T		not specified	Uncertain significance (Nov 09, 2021)
12-56952150-C-G		not specified	Uncertain significance (Nov 13, 2023)
12-56952150-C-T		not specified	Uncertain significance (Feb 07, 2023)
12-56952151-G-C		not specified	Uncertain significance (Mar 24, 2023)
12-56952171-G-A		not specified	Uncertain significance (Jan 17, 2024)
12-56952839-A-G		not specified	Uncertain significance (Aug 02, 2023)
12-56952847-C-T		not specified	Uncertain significance (May 14, 2024)
12-56952896-A-G		not specified	Uncertain significance (Jun 03, 2022)
12-56952931-G-T		not specified	Uncertain significance (Dec 17, 2023)
12-56952956-T-C		not specified	Likely benign (Mar 02, 2023)
12-56952967-AC-A			Benign (Mar 30, 2018)
12-56954960-C-T		not specified	Uncertain significance (Mar 15, 2024)
12-56954963-A-G		not specified	Uncertain significance (Aug 03, 2022)
12-56954970-A-G		not specified	Uncertain significance (May 17, 2023)
12-56954973-C-T		not specified	Uncertain significance (Feb 15, 2023)
12-56954975-C-T		not specified	Uncertain significance (Oct 19, 2021)
12-56954979-C-G		not specified	Uncertain significance (Jan 07, 2022)
12-56954990-G-T		not specified	Uncertain significance (Nov 02, 2023)
12-56955005-C-T		not specified	Uncertain significance (Oct 06, 2023)
12-56955025-T-G		not specified	Uncertain significance (Nov 28, 2023)
12-56955056-A-T		not specified	Uncertain significance (Apr 29, 2024)
12-56955122-G-A		not specified	Uncertain significance (May 06, 2024)
12-56955137-C-G		not specified	Uncertain significance (Sep 26, 2023)
12-56955150-C-T		not specified	Uncertain significance (Dec 19, 2023)
12-56957167-T-C		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RDH16	protein_coding	protein_coding	ENST00000398138	4	7940

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.39e-7	0.224	124936	10	800	125746	0.00323

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0955	189	185	1.02	0.0000111	2037
Missense in Polyphen		56	54.851	1.0209		653
Synonymous	0.837	71	80.6	0.881	0.00000508	662
Loss of Function	0.142	10	10.5	0.953	5.43e-7	122

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00768	0.00768
Ashkenazi Jewish	0.00477	0.00477
East Asian	0.0259	0.0250
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000159	0.000149
Middle Eastern	0.0259	0.0250
South Asian	0.000886	0.000850
Other	0.00116	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Oxidoreductase with a preference for NAD. Oxidizes all- trans-retinol and 13-cis-retinol to the corresponding aldehydes. Has higher activity towards CRBP-bound retinol than with free retinol. Oxidizes 3-alpha-hydroxysteroids. Oxidizes androstanediol and androsterone to dihydrotestosterone and androstanedione. Can also catalyze the reverse reaction. {ECO:0000269|PubMed:10329026, ECO:0000269|PubMed:12534290, ECO:0000269|PubMed:9677409}.
• Pathway: Retinol metabolism - Homo sapiens (human);Vitamin A Deficiency;Retinol Metabolism;Signaling by GPCR;Signal Transduction;RA biosynthesis pathway;The canonical retinoid cycle in rods (twilight vision);retinoate biosynthesis I;Signaling by Retinoic Acid;Signaling by Nuclear Receptors;G alpha (i) signalling events;Visual phototransduction;GPCR downstream signalling (Consensus)

Intolerance Scores

• loftool: 0.281
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.142
• hipred: N
• hipred_score: 0.146
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.180

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rdh9
• Phenotype: normal phenotype

Gene ontology

• Biological process: lipid metabolic process;electron transport chain
• Cellular component: endoplasmic reticulum membrane;integral component of membrane;organelle membrane;intracellular membrane-bounded organelle
• Molecular function: retinol dehydrogenase activity;electron transfer activity