RDH14

retinol dehydrogenase 14, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 2:18554723-18560679

Links

ENSG00000240857 ∙ NCBI:57665 ∙ OMIM:616796 ∙ HGNC:19979 ∙ Uniprot:Q9HBH5 ∙ 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 RDH14 gene.

• not_specified (66 variants)
• Intellectual_disability (1 variants)
• Cerebellar_atrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RDH14 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020905.4. 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						0
missense			64	2		66
nonsense						0
start loss						0
frameshift		1				1
splice donor/acceptor (+/-2bp)						0
Total	0	1	64	2	0

Highest pathogenic variant AF is 0.00006343752

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RDH14	protein_coding	protein_coding	ENST00000381249	2	5958

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000170	0.265	125724	0	19	125743	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.817	183	154	1.18	0.00000801	2130
Missense in Polyphen		54	54.077	0.99857		717
Synonymous	-0.166	64	62.3	1.03	0.00000322	718
Loss of Function	-0.142	7	6.61	1.06	2.82e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000333	0.000333
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000881	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Exhibits an oxidoreductive catalytic activity towards retinoids. Most efficient as an NADPH-dependent retinal reductase. Displays high activity toward 9-cis and all-trans-retinol. No steroid dehydrogenase activity detected. {ECO:0000269|PubMed:12226107}.
• Pathway: Signal Transduction;RA biosynthesis pathway;adenosine nucleotides degradation;purine nucleotides degradation;Signaling by Retinoic Acid;Signaling by Nuclear Receptors (Consensus)

Recessive Scores

• pRec: 0.156

Haploinsufficiency Scores

• pHI: 0.738
• hipred: N
• hipred_score: 0.292
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rdh14

Gene ontology

• Biological process: osteoblast differentiation;retinol metabolic process;oxidation-reduction process
• Cellular component: nucleus;lysosomal membrane;endoplasmic reticulum;endoplasmic reticulum membrane;membrane
• Molecular function: NADP-retinol dehydrogenase activity