RDH8

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

Basic information

Region (hg38): 19:10013249-10022279

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_specified (16 variants)
• not_provided (5 variants)
• STARGARDT_DISEASE_5 (1 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. These statistics are base on transcript: NM_000015725.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1		2	3
missense			13	2	2	17
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)	1		2			3
Total	1	0	17	2	4

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
		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

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

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