SDR9C7

protein-coding

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

Gene summary

This gene encodes a protein with similarity to the short-chain dehydrogenase/reductase (SDR) family but has not been shown to have retinoid or dehydrogenase activities. [provided by RefSeq, Apr 2010]

MANE transcript

NM_148897.3

Inheritance

ClinVar variants

P:9U:70B:32

Top phenotype

Ichthyosis, congenital, autosomal recessive 13

gnomAD constraint

pLI —, LoF o/e 0.42

Max pathogenic AF

—

Genomic locus

chr12:56,923,133-56,934,408

External References & Databases

Ensembl (ENSG00000170426)

Transcript & Mutation Effects

hg38 • Region Span ~11.3 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

ichthyosis, congenital, autosomal recessive 13STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0033092

Submitter: Labcorp Genetics (formerly Invitae)

ichthyosis, congenital, autosomal recessive 13MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0033092

Submitter: G2P

lamellar ichthyosisSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0017778

Submitter: Orphanet

ichthyosis, congenital, autosomal recessive 13STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0033092

Submitter: PanelApp Australia

ichthyosis, congenital, autosomal recessive 13STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0033092

Submitter: Genomics England PanelApp

Clinical Genomic Database (CGD)

Ichthyosis, congenital, autosomal recessive 13AR

Manifestation: Dermatologic

Intervention: General

Rationale: 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

Refs: 28173123

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SDR9C7 variants in ClinVar

9 Conditions Cataloged

Inborn genetic diseasesTotal: 61

not providedTotal: 57

Ichthyosis, congenital, autosomal recessive 13Total: 8

not specifiedTotal: 7

Lamellar ichthyosisTotal: 6

SDR9C7-related disorderTotal: 6

Congenital ichthyosis of skinTotal: 3

Ichthyosis and erythrokeratodermaTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_148897.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				17 clinvar	3 clinvar	20
missense	2 clinvar	4 clinvar	67 clinvar	9 clinvar	3 clinvar	85
nonsense	1 clinvar					1
start loss			1 clinvar			1
frameshift	1 clinvar		2 clinvar			3
splice donor/acceptor (+/-2bp)	1 clinvar					1
Total	5	4	70	26	6	111

Highest pathogenic variant AF is 0.00060098385

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_148897.3	RefSeq	NP_683695.1	4	MANE Select
ENST00000293502.2	Ensembl	ENSP00000293502.1	4	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signaling by GPCR
Signal Transduction
The canonical retinoid cycle in rods (twilight vision)
G alpha (i) signalling events
Visual phototransduction

Biological Process

oxidation-reduction process

Molecular Function

retinol dehydrogenase activity

Cellular Component

nucleolus
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000293502
Coding exons: 4
Length: 11252
Individuals with no LoFs: 125711
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 125735
p: 0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.633	172	197	0.873	0.0000120	2030
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.00039	0.00039	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0932

Intolerance Scores

LoFtool: 0.302
RVIS EVS: 0.33
RVIS percentile EVS: 73.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.209

Gene Damage Prediction

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