SDR9C7

short chain dehydrogenase/reductase family 9C member 7, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 12:56923133-56934408

Links

ENSG00000170426NCBI:121214OMIM:609769HGNC:29958Uniprot:Q8NEX9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • ichthyosis, congenital, autosomal recessive 13 (Strong), mode of inheritance: AR
  • ichthyosis, congenital, autosomal recessive 13 (Strong), mode of inheritance: AR
  • lamellar ichthyosis (Supportive), mode of inheritance: AR
  • ichthyosis, congenital, autosomal recessive 13 (Strong), mode of inheritance: AR
  • ichthyosis, congenital, autosomal recessive 13 (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Ichthyosis, congenital, autosomal recessive 13ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingDermatologic28173123

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SDR9C7 gene.

  • Inborn_genetic_diseases (57 variants)
  • not_provided (36 variants)
  • Ichthyosis,_congenital,_autosomal_recessive_13 (7 variants)
  • Lamellar_ichthyosis (6 variants)
  • not_specified (6 variants)
  • Congenital_ichthyosis_of_skin (3 variants)
  • SDR9C7-related_disorder (3 variants)
  • Ichthyosis_and_erythrokeratoderma (2 variants)
  • Intellectual_disability,_autosomal_recessive_53 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDR9C7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000148897.3. 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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
3
clinvar
6
missense
1
clinvar
5
clinvar
63
clinvar
7
clinvar
3
clinvar
79
nonsense
1
clinvar
1
start loss
1
1
frameshift
1
clinvar
2
clinvar
3
splice donor/acceptor (+/-2bp)
0
Total 3 5 66 10 6

Highest pathogenic variant AF is 0.000600984

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SDR9C7protein_codingprotein_codingENST00000293502 411252
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.01230.9561257110241257350.0000954
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6331721970.8730.00001202030
Missense in Polyphen5267.4680.77073715
Synonymous0.1027576.10.9850.00000449650
Loss of Function1.87512.00.4185.91e-7135

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002890.0000289
Ashkenazi Jewish0.0001000.0000992
East Asian0.0001630.000163
Finnish0.000.00
European (Non-Finnish)0.00006170.0000615
Middle Eastern0.0001630.000163
South Asian0.0003920.000392
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Displays weak conversion of all-trans-retinal to all- trans-retinol in the presence of NADH. Has apparently no steroid dehydrogenase activity. {ECO:0000269|PubMed:19703561}.;
Pathway
Signaling by GPCR;Signal Transduction;The canonical retinoid cycle in rods (twilight vision);G alpha (i) signalling events;Visual phototransduction;GPCR downstream signalling (Consensus)

Recessive Scores

pRec
0.0932

Intolerance Scores

loftool
0.302
rvis_EVS
0.33
rvis_percentile_EVS
73.54

Haploinsufficiency Scores

pHI
hipred
N
hipred_score
0.155
ghis
0.466

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.209

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sdr9c7
Phenotype

Gene ontology

Biological process
oxidation-reduction process
Cellular component
nucleolus;cytosol
Molecular function
retinol dehydrogenase activity