SDR39U1

protein-coding

short chain dehydrogenase/reductase family 39U member 1, the group of Short chain dehydrogenase/reductase superfamily

Gene summary

This gene encodes a member of the short-chain dehydrogenases/reductases (SDR) superfamily, which includes both classical and extended types. The encoded protein represents an extended type, with similarity to epimerases. Alternatively spliced transcript variants that encode different protein isoforms have been described. [provided by RefSeq, Mar 2014]

Previous symbols:

C14orf124

MANE transcript

NM_020195.3

Inheritance

—

ClinVar variants

U:59B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.07

Max pathogenic AF

—

Genomic locus

chr14:24,439,766-24,442,905

External References & Databases

Ensembl (ENSG00000100445)

Transcript & Mutation Effects

hg38 • Region Span ~3.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SDR39U1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 58

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020195.3. 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						0
missense			58 clinvar	3 clinvar		61
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	59	3	0	62

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 45 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020195.3	RefSeq	NP_064580.2	6	MANE Select
ENST00000399395.8	Ensembl	ENSP00000382327.3	6	MANE Select
NM_001290292.3	RefSeq	NP_001277221.1	3	Standard
NM_001290293.3	RefSeq	NP_001277222.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

oxidation-reduction process

Molecular Function

oxidoreductase activity

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000399395
Coding exons: 6
Length: 3140
Individuals with no LoFs: 124134
Homozygous LoFs: 0
Heterozygous LoFs: 517
Defined: 124651
p: 0.00208

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.292	187	176	1.06	0.00000964	1833
Missense (PolyPhen)		53	56.434	0.93915		538
Synonymous	0.622	67	73.8	0.908	0.00000396	654
Loss of Function	-0.259	16	14.9	1.07	9.02e-7	130

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00075	0.00071	rare
Latino/Admixed American	0.0011	0.0011	notable
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.0066	0.0066	notable
Finnish	0.00024	0.00023	rare
European (Non-Finnish)	0.0028	0.0027	notable
South Asian	0.0010	0.00098	notable
Other	0.0015	0.0015	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Putative NADP-dependent oxidoreductase. {ECO:0000305}.;

Recessive Scores

pRec: 0.0969

Intolerance Scores

LoFtool: 0.543
RVIS EVS: 1.46
RVIS percentile EVS: 95.21

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.560

Gene Damage Prediction

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