SDR39U1

short chain dehydrogenase/reductase family 39U member 1, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 14:24439766-24442905

Previous symbols: [ "C14orf124" ]

Links

ENSG00000100445 ∙ NCBI:56948 ∙ OMIM:616162 ∙ HGNC:20275 ∙ Uniprot:Q9NRG7 ∙ 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 SDR39U1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDR39U1 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						0
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	1	0

Variants in SDR39U1

This is a list of pathogenic ClinVar variants found in the SDR39U1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-24440131-C-G		not specified	Uncertain significance (Sep 25, 2024)
14-24440174-C-T		not specified	Uncertain significance (Sep 26, 2024)
14-24440180-A-G		not specified	Uncertain significance (Mar 21, 2023)
14-24440193-C-T		not specified	Uncertain significance (Nov 09, 2023)
14-24440195-C-T		not specified	Uncertain significance (Aug 20, 2024)
14-24440205-C-T		not specified	Uncertain significance (May 26, 2023)
14-24440214-C-T		not specified	Uncertain significance (May 30, 2024)
14-24440226-C-A		not specified	Uncertain significance (Mar 02, 2023)
14-24440235-G-C		not specified	Likely benign (Jan 18, 2025)
14-24440249-C-T		not specified	Uncertain significance (Dec 20, 2023)
14-24440253-G-A		not specified	Uncertain significance (May 02, 2024)
14-24440362-G-C		not specified	Uncertain significance (Mar 04, 2024)
14-24440378-C-A		not specified	Uncertain significance (Apr 18, 2023)
14-24440379-C-T		not specified	Likely benign (Mar 06, 2025)
14-24440415-C-T		not specified	Uncertain significance (Mar 14, 2023)
14-24440424-C-A		not specified	Uncertain significance (Sep 01, 2021)
14-24440438-C-T		not specified	Uncertain significance (Aug 02, 2024)
14-24440439-G-A		not specified	Uncertain significance (Jun 13, 2023)
14-24440453-A-G		not specified	Uncertain significance (May 15, 2023)
14-24440789-G-A		not specified	Uncertain significance (Nov 25, 2024)
14-24441679-C-T		not specified	Uncertain significance (Sep 14, 2022)
14-24441686-C-G		not specified	Uncertain significance (Feb 16, 2023)
14-24441698-C-A		not specified	Uncertain significance (Nov 24, 2024)
14-24441713-G-A		not specified	Uncertain significance (Nov 04, 2023)
14-24441739-A-C		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SDR39U1	protein_coding	protein_coding	ENST00000399395	6	3140

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.53e-11	0.0297	124134	0	517	124651	0.00208

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.292	187	176	1.06	0.00000964	1833
Missense in Polyphen		53	56.434	0.93915		538
Synonymous	0.622	67	73.8	0.908	0.00000396	654
Loss of Function	-0.259	16	14.9	1.07	9.02e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00187	0.00183
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.00663	0.00664
Finnish	0.000237	0.000232
European (Non-Finnish)	0.00282	0.00268
Middle Eastern	0.00663	0.00664
South Asian	0.00101	0.000981
Other	0.00152	0.00149

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative NADP-dependent oxidoreductase. {ECO:0000305}.

Recessive Scores

• pRec: 0.0969

Intolerance Scores

• loftool: 0.543
• rvis_EVS: 1.46
• rvis_percentile_EVS: 95.21

Haploinsufficiency Scores

• pHI: 0.0930
• hipred: N
• hipred_score: 0.219
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.560

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sdr39u1

Gene ontology

• Biological process: oxidation-reduction process
• Cellular component: nucleus
• Molecular function: oxidoreductase activity