DHRS3

dehydrogenase/reductase 3, the group of Short chain dehydrogenase/reductase superfamily|MicroRNA protein coding host genes

Basic information

Region (hg38): 1:12567909-12620133

Links

ENSG00000162496

∙ NCBI:9249 ∙ OMIM:612830 ∙ HGNC:17693 ∙ Uniprot:O75911 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

craniosynostosis (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DHRS3 gene.

not_specified (46 variants)
DHRS3-related_disorder (4 variants)
DHRS3_Deficiency (3 variants)
not_provided (1 variants)
Craniosynostosis_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DHRS3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004753.7. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense	1 clinvar		45 clinvar	4 clinvar	1 clinvar	51
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	45	5	1

Highest pathogenic variant AF is 0.000008676435

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DHRS3	protein_coding	protein_coding	ENST00000376223	6	49799

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.226	0.767	125707	0	4	125711	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.48	133	190	0.699	0.0000111	1942
Missense in Polyphen		35	68.882	0.50812		687
Synonymous	0.579	78	84.8	0.920	0.00000518	643
Loss of Function	2.32	3	11.5	0.261	4.90e-7	137

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000190	0.0000176
Middle Eastern	0.0000546	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalyzes the reduction of all-trans-retinal to all- trans-retinol in the presence of NADPH. {ECO:0000269|PubMed:9705317}.;
Pathway: Retinol metabolism - Homo sapiens (human);Vitamin A Deficiency;Retinol Metabolism;Vitamin A and Carotenoid Metabolism;Signaling by GPCR;Signal Transduction;RA biosynthesis pathway;Validated transcriptional targets of TAp63 isoforms;retinol biosynthesis;Signaling by Retinoic Acid;Signaling by Nuclear Receptors;The retinoid cycle in cones (daylight vision);G alpha (i) signalling events;Visual phototransduction;the visual cycle I (vertebrates);GPCR downstream signalling (Consensus)

Recessive Scores

pRec: 0.169

Intolerance Scores

loftool: 0.0298
rvis_EVS: -0.34
rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

pHI: 0.235
hipred: Y
hipred_score: 0.728
ghis: 0.554

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.945

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Dhrs3
Phenotype: vision/eye 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); digestive/alimentary phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); growth/size/body region phenotype; craniofacial phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process: retinoid metabolic process;outflow tract morphogenesis;visual perception;electron transport chain;regulation of ossification;retinol metabolic process;regulation of retinoic acid receptor signaling pathway;negative regulation of retinoic acid receptor signaling pathway;roof of mouth development;bone morphogenesis;cardiac septum morphogenesis
Cellular component: endoplasmic reticulum membrane;lipid droplet;integral component of membrane;photoreceptor outer segment membrane
Molecular function: nucleotide binding;retinol dehydrogenase activity;electron transfer activity;NADP-retinol dehydrogenase activity