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.

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.

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				1	1	2
missense			29	1		30
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	30	2	1

Variants in DHRS3

This is a list of pathogenic ClinVar variants found in the DHRS3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-12568347-C-A		not specified	Uncertain significance (Nov 20, 2024)
1-12568377-G-A		not specified	Uncertain significance (Mar 04, 2025)
1-12568380-C-T		not specified	Uncertain significance (Nov 06, 2023)
1-12568411-C-T		not specified	Uncertain significance (Dec 07, 2021)
1-12568423-T-G		not specified	Uncertain significance (May 24, 2024)
1-12572741-C-G		not specified	Uncertain significance (Feb 27, 2024)
1-12572741-C-T		not specified	Likely benign (Nov 06, 2023)
1-12572746-G-A		not specified	Uncertain significance (May 26, 2023)
1-12572806-C-A		not specified	Uncertain significance (Sep 25, 2024)
1-12572809-C-T		not specified	Uncertain significance (Jan 27, 2025)
1-12572822-C-G		DHRS3 Deficiency	Uncertain significance (Jan 22, 2025)
1-12572824-G-A		not specified	Uncertain significance (Jan 20, 2023)
1-12572834-G-C		not specified	Uncertain significance (Jun 11, 2021)
1-12578749-T-C		not specified	Uncertain significance (Aug 30, 2021)
1-12578776-C-T		not specified	Uncertain significance (May 06, 2024)
1-12578787-G-A		not specified	Uncertain significance (May 12, 2024)
1-12578890-C-T		not specified	Uncertain significance (Oct 12, 2021)
1-12578891-G-A			Likely benign (Jul 01, 2022)
1-12578905-C-T		DHRS3 Deficiency	Pathogenic (Jan 22, 2025)
1-12578909-G-C		not specified	Uncertain significance (Oct 12, 2021)
1-12578936-C-T			Benign (Dec 31, 2019)
1-12579283-T-G		DHRS3-related disorder	Benign (Mar 22, 2019)
1-12579304-C-T		DHRS3-related disorder	Uncertain significance (Nov 08, 2022)
1-12579378-G-C		not specified	Uncertain significance (Jan 23, 2024)
1-12579379-C-T		not specified	Uncertain significance (Sep 16, 2021)

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