RDH8

retinol dehydrogenase 8, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 19:10013248-10022279

Links

ENSG00000080511 ∙ NCBI:50700 ∙ OMIM:608575 ∙ HGNC:14423 ∙ Uniprot:Q9NYR8 ∙ 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 RDH8 gene.

• not provided (5 variants)
• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RDH8 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			3	1	2	6
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	1	4

Variants in RDH8

This is a list of pathogenic ClinVar variants found in the RDH8 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-10013577-A-G			Benign (Jul 31, 2018)
19-10017190-T-C			Benign (Jul 31, 2018)
19-10017206-G-C		not specified	Uncertain significance (Feb 05, 2024)
19-10018742-G-A		not specified	Uncertain significance (Mar 01, 2023)
19-10018742-G-C		not specified	Uncertain significance (Feb 07, 2023)
19-10018879-C-T			Benign (Jul 15, 2018)
19-10020730-A-T			Likely benign (Jun 13, 2018)
19-10021436-C-T		not specified	Uncertain significance (Jan 24, 2023)
19-10021612-C-T		not specified	Uncertain significance (Feb 21, 2024)
19-10021673-G-A		not specified	Uncertain significance (Aug 04, 2023)
19-10021730-C-T			Benign (Jul 31, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RDH8	protein_coding	protein_coding	ENST00000591589	6	9031

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00117	0.854	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.258	201	212	0.950	0.0000139	2104
Missense in Polyphen		71	78.63	0.90296		844
Synonymous	0.126	89	90.5	0.983	0.00000608	725
Loss of Function	1.26	6	10.4	0.578	4.40e-7	125

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000395	0.000394
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000534	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.000273	0.000261
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Retinol dehydrogenase with a clear preference for NADP. Converts all-trans-retinal to all-trans-retinol. May play a role in the regeneration of visual pigment at high light intensity (By similarity). {ECO:0000250}.
• Pathway: Retinol metabolism - Homo sapiens (human);Vitamin A Deficiency;Retinol Metabolism;Vitamin A and Carotenoid Metabolism;Signaling by GPCR;Signal Transduction;Androgen and estrogen biosynthesis and metabolism;The canonical retinoid cycle in rods (twilight vision);C21-steroid hormone biosynthesis and metabolism;retinol biosynthesis;G alpha (i) signalling events;Visual phototransduction;the visual cycle I (vertebrates);GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• rvis_EVS: 0.69
• rvis_percentile_EVS: 85.18

Haploinsufficiency Scores

• pHI: 0.341
• hipred: N
• hipred_score: 0.197

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0936

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rdh8
• Phenotype: pigmentation phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: steroid biosynthetic process;estrogen biosynthetic process;visual perception;retinol metabolic process;response to stimulus;oxidation-reduction process
• Cellular component: cytoplasm;integral component of plasma membrane
• Molecular function: estradiol 17-beta-dehydrogenase activity;retinol dehydrogenase activity;NADP-retinol dehydrogenase activity