SDR42E1

short chain dehydrogenase/reductase family 42E, member 1, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 16:81988854-82011481

Links

ENSG00000184860 ∙ NCBI:93517 ∙ OMIM:616164 ∙ HGNC:29834 ∙ Uniprot:Q8WUS8 ∙ 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 SDR42E1 gene.

• Inborn genetic diseases (23 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDR42E1 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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	0

Variants in SDR42E1

This is a list of pathogenic ClinVar variants found in the SDR42E1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-81999121-A-G		not specified	Uncertain significance (Dec 20, 2021)
16-81999130-G-A		not specified	Uncertain significance (Mar 08, 2024)
16-81999140-G-T		not specified	Uncertain significance (Oct 19, 2021)
16-81999182-C-G		not specified	Uncertain significance (Apr 07, 2023)
16-81999202-G-A		not specified	Uncertain significance (Nov 18, 2022)
16-81999229-T-C		not specified	Uncertain significance (May 01, 2022)
16-81999293-G-T		not specified	Uncertain significance (Jul 26, 2022)
16-81999418-A-G		not specified	Uncertain significance (Oct 05, 2021)
16-81999493-C-T		not specified	Uncertain significance (Nov 05, 2021)
16-81999505-A-G		not specified	Uncertain significance (May 09, 2023)
16-81999506-A-T		not specified	Uncertain significance (May 09, 2023)
16-81999515-C-G		not specified	Uncertain significance (Nov 17, 2022)
16-81999548-C-T		not specified	Uncertain significance (Feb 28, 2024)
16-81999560-G-A		not specified	Uncertain significance (Aug 05, 2023)
16-81999641-T-C		not specified	Uncertain significance (Nov 30, 2022)
16-81999650-C-A		not specified	Uncertain significance (Mar 27, 2023)
16-81999659-C-T		not specified	Uncertain significance (Dec 12, 2023)
16-81999682-A-G		not specified	Uncertain significance (May 31, 2023)
16-81999792-A-C		not specified	Uncertain significance (Sep 23, 2023)
16-81999857-G-T		not specified	Uncertain significance (Jan 03, 2024)
16-81999868-T-C		not specified	Uncertain significance (Apr 13, 2023)
16-81999940-A-G		not specified	Uncertain significance (Jul 25, 2023)
16-81999991-C-G		not specified	Uncertain significance (May 17, 2023)
16-82000018-C-T		not specified	Uncertain significance (Dec 07, 2021)
16-82000043-T-C		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SDR42E1	protein_coding	protein_coding	ENST00000328945	2	13873

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.56e-9	0.0329	100728	1648	22421	124797	0.102

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.78	287	214	1.34	0.0000119	2554
Missense in Polyphen		102	79.556	1.2821		1022
Synonymous	-1.89	109	86.6	1.26	0.00000494	822
Loss of Function	-0.794	12	9.38	1.28	5.34e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0873	0.0869
Ashkenazi Jewish	0.120	0.119
East Asian	0.00206	0.00206
Finnish	0.0910	0.0791
European (Non-Finnish)	0.130	0.129
Middle Eastern	0.00206	0.00206
South Asian	0.161	0.160
Other	0.115	0.114

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0737

Intolerance Scores

• loftool: 0.179
• rvis_EVS: 1.2
• rvis_percentile_EVS: 92.98

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.216
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.146

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sdr42e1

Gene ontology

• Biological process: steroid biosynthetic process;oxidation-reduction process
• Cellular component: integral component of membrane
• Molecular function: 3-beta-hydroxy-delta5-steroid dehydrogenase activity;oxidoreductase activity;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor