SDR9C7

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

Basic information

Region (hg38): 12:56923132-56934408

Links

ENSG00000170426 ∙ NCBI:121214 ∙ OMIM:609769 ∙ HGNC:29958 ∙ Uniprot:Q8NEX9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ichthyosis, congenital, autosomal recessive 13	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic	28173123

ClinVar

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

• Ichthyosis, congenital, autosomal recessive 13 (2 variants)
• not provided (2 variants)
• Congenital ichthyosis of skin (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.

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				3	3	6
missense		2	35	4	3	44
nonsense	1					1
start loss			1			1
frameshift	1		2			3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					1	1
Total	2	2	38	7	7

Highest pathogenic variant AF is 0.00000657

Variants in SDR9C7

This is a list of pathogenic ClinVar variants found in the SDR9C7 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-56923872-G-C		Inborn genetic diseases	Uncertain significance (Jun 05, 2024)
12-56923886-CA-C		not specified	Uncertain significance (Nov 15, 2022)
12-56923899-C-CTT			Uncertain significance (Sep 13, 2022)
12-56923936-C-T			Uncertain significance (Dec 16, 2021)
12-56923940-G-T		Inborn genetic diseases	Uncertain significance (May 08, 2024)
12-56923941-G-T		Inborn genetic diseases	Uncertain significance (Dec 16, 2022)
12-56923942-T-C		Inborn genetic diseases	Uncertain significance (Mar 23, 2022)
12-56923949-G-A		Lamellar ichthyosis	Pathogenic (May 23, 2024)
12-56923954-C-T		Inborn genetic diseases	Uncertain significance (Mar 03, 2022)
12-56923955-G-A			Uncertain significance (Sep 26, 2021)
12-56923963-C-T		Inborn genetic diseases	Uncertain significance (Aug 04, 2023)
12-56923973-T-C		Inborn genetic diseases	Likely benign (Sep 13, 2023)
12-56929396-G-A		Inborn genetic diseases	Conflicting classifications of pathogenicity (Nov 15, 2022)
12-56929403-A-T			Uncertain significance (Oct 17, 2022)
12-56929412-G-A			Likely benign (Dec 31, 2019)
12-56929415-G-C			Uncertain significance (Jun 14, 2021)
12-56929422-C-T			Benign (Jan 15, 2024)
12-56929423-G-A		Inborn genetic diseases	Uncertain significance (Mar 14, 2024)
12-56929431-T-C		Inborn genetic diseases	Uncertain significance (Jan 19, 2024)
12-56929435-G-A			Uncertain significance (Oct 07, 2022)
12-56929439-C-G		Inborn genetic diseases	Uncertain significance (Jul 13, 2022)
12-56929455-C-T			Benign (Jan 05, 2024)
12-56929456-G-A		Ichthyosis, congenital, autosomal recessive 13 • Congenital ichthyosis of skin	Pathogenic (Aug 25, 2022)
12-56929462-G-A		Inborn genetic diseases	Uncertain significance (Nov 30, 2022)
12-56929484-G-A			Benign (Oct 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SDR9C7	protein_coding	protein_coding	ENST00000293502	4	11252

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0123	0.956	125711	0	24	125735	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.633	172	197	0.873	0.0000120	2030
Missense in Polyphen		52	67.468	0.77073		715
Synonymous	0.102	75	76.1	0.985	0.00000449	650
Loss of Function	1.87	5	12.0	0.418	5.91e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.000163	0.000163
South Asian	0.000392	0.000392
Other	0.00	0.00

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

• 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

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

Mouse Genome Informatics

• Gene name: Sdr9c7

Gene ontology

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