SDR16C5

short chain dehydrogenase/reductase family 16C member 5, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 8:56300005-56320776

Links

ENSG00000170786 ∙ NCBI:195814 ∙ OMIM:608989 ∙ HGNC:30311 ∙ Uniprot:Q8N3Y7 ∙ 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 SDR16C5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDR16C5 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	2		25
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	2	0

Variants in SDR16C5

This is a list of pathogenic ClinVar variants found in the SDR16C5 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-56305618-T-C		not specified	Uncertain significance (May 25, 2022)
8-56305631-G-T		not specified	Uncertain significance (Aug 17, 2021)
8-56305644-C-T		not specified	Uncertain significance (Dec 28, 2022)
8-56305682-C-A		not specified	Uncertain significance (Jan 26, 2023)
8-56305697-C-T		not specified	Uncertain significance (May 01, 2024)
8-56306710-T-C		not specified	Uncertain significance (Aug 21, 2023)
8-56306757-A-G		not specified	Likely benign (Dec 16, 2022)
8-56306758-C-G		not specified	Uncertain significance (Oct 29, 2021)
8-56308963-C-G		not specified	Uncertain significance (Dec 10, 2024)
8-56308994-T-G		not specified	Uncertain significance (Jul 27, 2024)
8-56312162-A-C		not specified	Uncertain significance (Oct 06, 2022)
8-56312255-T-A		not specified	Uncertain significance (Sep 14, 2022)
8-56312273-C-T		not specified	Uncertain significance (Oct 29, 2021)
8-56316016-T-C		not specified	Uncertain significance (Apr 25, 2023)
8-56316052-C-T		not specified	Uncertain significance (Nov 07, 2022)
8-56316058-C-T		not specified	Uncertain significance (Sep 29, 2023)
8-56316062-T-G		not specified	Uncertain significance (Nov 15, 2024)
8-56316074-C-T		not specified	Uncertain significance (Mar 03, 2025)
8-56316094-C-T		not specified	Likely benign (Feb 06, 2024)
8-56316130-T-C		not specified	Uncertain significance (Nov 18, 2022)
8-56316157-C-G		not specified	Uncertain significance (Aug 29, 2024)
8-56316203-C-T		not specified	Uncertain significance (Oct 09, 2024)
8-56316212-T-C		not specified	Uncertain significance (May 28, 2024)
8-56316212-T-G		not specified	Uncertain significance (Jun 07, 2024)
8-56316230-C-G		not specified	Uncertain significance (Apr 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SDR16C5	protein_coding	protein_coding	ENST00000303749	6	20767

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0122	0.956	125672	0	76	125748	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.261	174	165	1.06	0.00000826	2017
Missense in Polyphen		70	65.587	1.0673		795
Synonymous	0.178	61	62.8	0.971	0.00000351	592
Loss of Function	1.86	5	11.9	0.419	5.01e-7	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00207	0.00180
Finnish	0.00	0.00
European (Non-Finnish)	0.0000794	0.0000791
Middle Eastern	0.00207	0.00180
South Asian	0.000818	0.000817
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Oxidoreductase with strong preference for NAD. Active in both the oxidative and reductive directions. Oxidizes all-trans- retinol in all-trans-retinaldehyde. No activity was detected with 11-cis-retinol or 11-cis-retinaldehyde as substrates with either NAD(+)/NADH or NADP(+)/NADPH. {ECO:0000269|PubMed:18926804}.
• Pathway: Retinol metabolism - Homo sapiens (human);Vitamin A and Carotenoid Metabolism;Signal Transduction;RA biosynthesis pathway;retinoate biosynthesis I;Signaling by Retinoic Acid;Signaling by Nuclear Receptors (Consensus)

Recessive Scores

• pRec: 0.0803

Intolerance Scores

• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.49

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.205
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.300

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sdr16c5

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;positive regulation of histone deacetylation;negative regulation of histone acetylation;retinol metabolic process;retinal metabolic process;keratinocyte proliferation;oxidation-reduction process
• Cellular component: chromatin;nucleus;endoplasmic reticulum;endoplasmic reticulum membrane;lipid droplet;plasma membrane;integral component of membrane;transcriptional repressor complex
• Molecular function: DNA-binding transcription factor activity;retinol dehydrogenase activity;transcription factor binding;activating transcription factor binding