RDH11

retinol dehydrogenase 11, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 14:67676800-67695793

Links

ENSG00000072042 ∙ NCBI:51109 ∙ OMIM:607849 ∙ HGNC:17964 ∙ Uniprot:Q8TC12 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• retinitis pigmentosa-juvenile cataract-short stature-intellectual disability syndrome (Supportive), mode of inheritance: AR
• retinitis pigmentosa-juvenile cataract-short stature-intellectual disability syndrome (Limited), mode of inheritance: AR
• retinitis pigmentosa-juvenile cataract-short stature-intellectual disability syndrome (Limited), mode of inheritance: AR
• retinitis pigmentosa-juvenile cataract-short stature-intellectual disability syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Microphthalmia, isolated, with coloboma 10; Retinal dystrophy, juvenile cataracts, and short stature syndrome	AD/AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	24916380; 25910211

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RDH11 gene.

• not_provided (192 variants)
• not_specified (36 variants)
• RDH11-related_disorder (6 variants)
• Retinitis_pigmentosa-juvenile_cataract-short_stature-intellectual_disability_syndrome (5 variants)
• Retinal_dystrophy (1 variants)
• Optic_atrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RDH11 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016026.4. 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				44	1	45
missense			115	4	1	120
nonsense	4	1				5
start loss						0
frameshift	2		2			4
splice donor/acceptor (+/-2bp)			1			1
Total	6	1	118	48	2

Highest pathogenic variant AF is 0.000014250787

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RDH11	protein_coding	protein_coding	ENST00000381346	7	19014

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.08e-7	0.341	125724	0	23	125747	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.554	158	179	0.883	0.00000970	2052
Missense in Polyphen		70	80.029	0.87468		932
Synonymous	-0.781	82	73.5	1.12	0.00000406	660
Loss of Function	0.597	12	14.4	0.831	7.32e-7	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000118	0.000114
Middle Eastern	0.000109	0.000109
South Asian	0.0000658	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Exhibits an oxidoreductive catalytic activity towards retinoids. Most efficient as an NADPH-dependent retinal reductase. Displays high activity towards 9-cis and all-trans-retinol. Also involved in the metabolism of short-chain aldehydes. No steroid dehydrogenase activity detected.
• Disease: DISEASE: Retinal dystrophy, juvenile cataracts, and short stature syndrome (RDJCSS) [MIM:616108]: A disorder characterized by retinal dystrophy resulting in progressive decrease in visual acuity and difficulties with night vision in the first decade of life, development of juvenile cataracts, facial dysmorphism, psychomotor developmental delays, learning disabilities and short stature. Ophthalmological findings include salt-and-pepper retinopathy, attenuation of the arterioles, generalized rod-cone dysfunction, mottled macula at an early age, and peripapillary sparing of the retinal pigment epithelium. {ECO:0000269|PubMed:24916380}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Retinol metabolism - Homo sapiens (human);Vitamin A Deficiency;Retinol Metabolism;Signaling by GPCR;Signal Transduction;Metabolism of fat-soluble vitamins;RA biosynthesis pathway;Metabolism;The canonical retinoid cycle in rods (twilight vision);Metabolism of vitamins and cofactors;retinol biosynthesis;Signaling by Retinoic Acid;Signaling by Nuclear Receptors;Retinoid metabolism and transport;G alpha (i) signalling events;Visual phototransduction;the visual cycle I (vertebrates);GPCR downstream signalling (Consensus)

Intolerance Scores

• loftool: 0.208
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.335
• hipred: N
• hipred_score: 0.199
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.689

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rdh11
• Phenotype: vision/eye phenotype

Gene ontology

• Biological process: retinoid metabolic process;adaptation of rhodopsin mediated signaling;retinol metabolic process;retinal metabolic process;oxidation-reduction process
• Cellular component: photoreceptor inner segment;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: retinol dehydrogenase activity;protein binding;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;NADP-retinol dehydrogenase activity