RDH13

retinol dehydrogenase 13, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 19:55039108-55071291

Links

ENSG00000160439 ∙ NCBI:112724 ∙ ∙ HGNC:19978 ∙ Uniprot:Q8NBN7 ∙ 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 RDH13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RDH13 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				3	1	4
missense			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	27	4	1

Variants in RDH13

This is a list of pathogenic ClinVar variants found in the RDH13 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55045103-A-C		not specified	Uncertain significance (Mar 16, 2022)
19-55045108-G-A		not specified	Uncertain significance (Oct 26, 2021)
19-55045127-G-A		not specified	Uncertain significance (Nov 08, 2022)
19-55045130-C-T		not specified	Uncertain significance (Feb 21, 2024)
19-55045151-G-A		not specified	Uncertain significance (Dec 14, 2023)
19-55045153-G-A		not specified	Uncertain significance (Dec 10, 2024)
19-55045175-C-T			Uncertain significance (Jan 27, 2016)
19-55045257-G-T		not specified	Uncertain significance (Oct 29, 2024)
19-55045269-G-T			Likely benign (Oct 01, 2022)
19-55047390-G-T		not specified	Uncertain significance (Jul 20, 2021)
19-55047392-G-A		not specified	Uncertain significance (Aug 14, 2024)
19-55047397-G-C		not specified	Uncertain significance (Oct 26, 2022)
19-55047438-G-A			Benign (Jun 08, 2018)
19-55047453-C-T		not specified	Uncertain significance (Mar 20, 2024)
19-55047461-T-C		not specified	Uncertain significance (Jul 26, 2024)
19-55048338-G-A		not specified	Uncertain significance (Sep 15, 2021)
19-55048348-C-G		not specified	Uncertain significance (Feb 10, 2022)
19-55048362-G-A		not specified	Uncertain significance (May 26, 2023)
19-55048366-G-A			Likely benign (Jan 01, 2023)
19-55048371-C-T		not specified	Uncertain significance (Aug 02, 2023)
19-55048392-C-T		not specified	Uncertain significance (Mar 18, 2024)
19-55048440-C-G		not specified	Uncertain significance (May 13, 2024)
19-55048469-G-A		not specified	Uncertain significance (Nov 13, 2024)
19-55048475-T-C		not specified	Uncertain significance (Nov 03, 2023)
19-55048699-G-A			Likely benign (Jun 08, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RDH13	protein_coding	protein_coding	ENST00000415061	7	32184

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.04e-14	0.00427	124684	0	114	124798	0.000457

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.586	232	208	1.11	0.0000135	2094
Missense in Polyphen		78	79.462	0.98161		751
Synonymous	-0.455	101	95.3	1.06	0.00000689	688
Loss of Function	-0.956	18	14.1	1.27	8.55e-7	149

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000675	0.000673
Ashkenazi Jewish	0.00	0.00
East Asian	0.00184	0.00184
Finnish	0.00	0.00
European (Non-Finnish)	0.000340	0.000327
Middle Eastern	0.00184	0.00184
South Asian	0.000662	0.000654
Other	0.000332	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Does not exhibit retinol dehydrogenase (RDH) activity in vitro.
• Pathway: Signal Transduction;RA biosynthesis pathway;Signaling by Retinoic Acid;Signaling by Nuclear Receptors (Consensus)

Intolerance Scores

• loftool: 0.318
• rvis_EVS: -0.04
• rvis_percentile_EVS: 50.45

Haploinsufficiency Scores

• pHI: 0.206
• hipred: N
• hipred_score: 0.229
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rdh13
• 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; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: response to high light intensity;retina layer formation;eye photoreceptor cell development;retinol metabolic process;oxidation-reduction process
• Cellular component: mitochondrial inner membrane
• Molecular function: NADP-retinol dehydrogenase activity