SDR39U1

Summary

SDR39U1 (short chain dehydrogenase/reductase family 39U member 1, HGNC:20275) is a protein-coding gene on chromosome 14q12, encoding Epimerase family protein SDR39U1 (Q9NRG7). Putative NADP-dependent oxidoreductase.

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.

Source: NCBI Gene 56948 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 17 total
• MANE Select transcript: NM_020195

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20275
Approved symbol	SDR39U1
Name	short chain dehydrogenase/reductase family 39U member 1
Location	14q12
Locus type	gene with protein product
Status	Approved
Aliases	HCDI
Ensembl gene	ENSG00000100445
Ensembl biotype	protein_coding
OMIM	616162
Entrez	56948

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 11 protein_coding, 9 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000399395, ENST00000538105, ENST00000544691, ENST00000553343, ENST00000553546, ENST00000553930, ENST00000553937, ENST00000554698, ENST00000554947, ENST00000555225, ENST00000555355, ENST00000555365, ENST00000555561, ENST00000555778, ENST00000555830, ENST00000556175, ENST00000556249, ENST00000556262, ENST00000556523, ENST00000556548, ENST00000556707, ENST00000859574

RefSeq mRNA: 10 — MANE Select: NM_020195 NM_001290292, NM_001290293, NM_001308075, NM_001387322, NM_001387323, NM_001387324, NM_001387325, NM_001387326, NM_001387327, NM_020195

CCDS: CCDS45091, CCDS73626, CCDS76665

Canonical transcript exons

ENST00000399395 — 6 exons

Exon	Start	End
ENSE00001735351	24442754	24442776
ENSE00003500874	24440783	24440926
ENSE00003568705	24442178	24442260
ENSE00003570363	24441674	24441795
ENSE00003606446	24442346	24442452
ENSE00003615338	24439766	24440492

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 97.96.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.1151 / max 297.1463, expressed in 1812 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
142610	15.2600	1797
142606	4.3435	1562
142605	3.5493	1441
142607	1.1771	754
142608	0.4118	208
142609	0.2043	69
142611	0.1691	46

Top tissues by expression

295 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
apex of heart	UBERON:0002098	97.96	gold quality
adenohypophysis	UBERON:0002196	97.65	gold quality
right hemisphere of cerebellum	UBERON:0014890	97.36	gold quality
pituitary gland	UBERON:0000007	97.30	gold quality
cerebellar hemisphere	UBERON:0002245	97.10	gold quality
cerebellar cortex	UBERON:0002129	97.05	gold quality
right adrenal gland cortex	UBERON:0035827	96.89	gold quality
right adrenal gland	UBERON:0001233	96.84	gold quality
left lobe of thyroid gland	UBERON:0001120	96.80	gold quality
metanephros cortex	UBERON:0010533	96.78	gold quality
left adrenal gland cortex	UBERON:0035825	96.73	gold quality
right lobe of thyroid gland	UBERON:0001119	96.67	gold quality
left adrenal gland	UBERON:0001234	96.64	gold quality
right uterine tube	UBERON:0001302	96.62	gold quality
hindlimb stylopod muscle	UBERON:0004252	96.61	gold quality
mucosa of stomach	UBERON:0001199	96.58	gold quality
adrenal cortex	UBERON:0001235	96.58	gold quality
right atrium auricular region	UBERON:0006631	96.46	gold quality
left ovary	UBERON:0002119	96.42	gold quality
right ovary	UBERON:0002118	96.35	gold quality
body of uterus	UBERON:0009853	96.34	gold quality
endocervix	UBERON:0000458	96.32	gold quality
cerebellum	UBERON:0002037	96.31	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	96.18	gold quality
spleen	UBERON:0002106	96.17	gold quality
lower esophagus mucosa	UBERON:0035834	96.15	gold quality
thyroid gland	UBERON:0002046	96.14	gold quality
lower esophagus muscularis layer	UBERON:0035833	96.11	gold quality
lower esophagus	UBERON:0013473	96.10	gold quality
ventricular zone	UBERON:0003053	96.09	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.46

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

19 targeting SDR39U1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-200A-5P	99.76	69.10	949
HSA-MIR-200B-5P	99.76	69.05	948
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-10394-5P	99.65	66.83	1852
HSA-MIR-1205	99.65	66.76	1826
HSA-MIR-3153	99.55	67.59	2337
HSA-MIR-671-5P	99.52	67.11	1277
HSA-MIR-548AV-3P	99.43	68.50	1721
HSA-MIR-548B-3P	99.38	67.26	1000
HSA-MIR-1286	99.09	66.23	1046
HSA-MIR-219A-1-3P	98.91	67.87	639
HSA-MIR-4684-5P	98.29	67.99	1650
HSA-MIR-204-3P	97.80	66.84	1656
HSA-MIR-4646-5P	97.70	66.84	1692

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	sdr39u1	ENSDARG00000099617
mus_musculus	Sdr39u1	ENSMUSG00000022223
rattus_norvegicus	Sdr39u1	ENSRNOG00000020544
drosophila_melanogaster	CG8768	FBGN0033769

Protein

Protein identifiers

Epimerase family protein SDR39U1 — Q9NRG7 (reviewed: Q9NRG7)

Alternative names: Short-chain dehydrogenase/reductase family 39U member 1

All UniProt accessions (10): Q9NRG7, F6RWC2, G3V2Z6, G3V3J5, G3V451, G3V4N6, G3V4Z0, G3V5T1, H0YJ71, Q86TZ5

UniProt curated annotations — full annotation on UniProt →

Function. Putative NADP-dependent oxidoreductase.

Tissue specificity. Expressed in adrenal gland.

Miscellaneous. Despite its name, it shares more sequence similarity with the sugar epimerase family than with the short-chain dehydrogenases/reductases (SDR) family.

Similarity. Belongs to the NAD(P)-dependent epimerase/dehydratase family. SDR39U1 subfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NRG7-2	1	yes
Q9NRG7-3	2

RefSeq proteins (10): NP_001277221, NP_001277222, NP_001295004, NP_001374251, NP_001374252, NP_001374253, NP_001374254, NP_001374255, NP_001374256, NP_064580* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001509	Epimerase_deHydtase	Domain
IPR010099	SDR39U1	Family
IPR013549	DUF1731	Domain
IPR036291	NAD(P)-bd_dom_sf	Homologous_superfamily

Pfam: PF01370, PF08338

UniProt features (34 total): helix 12, strand 9, binding site 5, sequence variant 4, splice variant 2, chain 1, turn 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
4B4O	X-RAY DIFFRACTION	2.7

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NRG7-F1	97.24	0.99

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (5): 31–32; 58–59; 77; 82; 160

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 111 (showing top): MORF_UBE2I, chr14q12, MORF_TERF1, MORF_AATF, MORF_PPP2CA, GAVIN_FOXP3_TARGETS_CLUSTER_P3, MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, MORF_PRKAG1, RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_D, BRUINS_UVC_RESPONSE_LATE, CHANGOLKAR_H2AFY_TARGETS_UP, RREB1_01, DLX4_TARGET_GENES, FEV_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (1): oxidoreductase activity (GO:0016491)

GO Cellular Component (2): nucleus (GO:0005634), mitochondrion (GO:0005739)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	2
catalytic activity	1
cytoplasm	1

Protein interactions and networks

STRING

798 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SDR39U1	NYNRIN	Q9P2P1	589
SDR39U1	TRMT2A	Q8IZ69	577
SDR39U1	STOML1	Q9UBI4	574
SDR39U1	GIMAP7	Q8NHV1	558
SDR39U1	TUBGCP6	Q96RT7	538
SDR39U1	STXBP6	Q8NFX7	513
SDR39U1	CBLN3	Q6UW01	511
SDR39U1	NCLN	Q969V3	490
SDR39U1	FCGR1BP	Q92637	446
SDR39U1	ZNF646	O15015	439
SDR39U1	AAGAB	Q6PD74	437
SDR39U1	ZDHHC24	Q6UX98	415
SDR39U1	ZNF473	Q8WTR7	414
SDR39U1	KHNYN	O15037	413
SDR39U1	LHFPL2	Q6ZUX7	412

IntAct

26 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
HSPD1	NUDT19	psi-mi:“MI:0914”(association)	0.710
BPNT1	GTPBP10	psi-mi:“MI:0914”(association)	0.530
SDR39U1	PPP1CC	psi-mi:“MI:0915”(physical association)	0.370
COQ9	NDUFS8	psi-mi:“MI:0914”(association)	0.350
COQ9	ACOT7	psi-mi:“MI:0914”(association)	0.350
HLA-DRA	TMEM223	psi-mi:“MI:0914”(association)	0.350
UQCRFS1	VWA8	psi-mi:“MI:0914”(association)	0.350
MALSU1	VWA8	psi-mi:“MI:0914”(association)	0.350
PRKY	METTL15	psi-mi:“MI:0914”(association)	0.350
MRPL12		psi-mi:“MI:0914”(association)	0.350
CCT8L2	DVL2	psi-mi:“MI:0914”(association)	0.350
SHC2	VWA8	psi-mi:“MI:0914”(association)	0.350
YARS2	VWA8	psi-mi:“MI:0914”(association)	0.350
AMACR	VWA8	psi-mi:“MI:0914”(association)	0.350
RASL10B	VWA8	psi-mi:“MI:0914”(association)	0.350
FAHD1	VWA8	psi-mi:“MI:0914”(association)	0.350
IMMP1L	NUDT19	psi-mi:“MI:2364”(proximity)	0.270
KCNK3	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
CFTR	UBA6	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (37): SDR39U1 (Affinity Capture-MS), SDR39U1 (Affinity Capture-MS), SDR39U1 (Affinity Capture-MS), SDR39U1 (Affinity Capture-MS), SDR39U1 (Affinity Capture-RNA), SDR39U1 (Proximity Label-MS), SDR39U1 (Positive Genetic), SDR39U1 (Affinity Capture-MS), SDR39U1 (Affinity Capture-MS), SDR39U1 (Affinity Capture-MS), SDR39U1 (Affinity Capture-MS), SDR39U1 (Affinity Capture-MS), SDR39U1 (Affinity Capture-MS), SDR39U1 (Affinity Capture-MS), SDR39U1 (Affinity Capture-MS)

ESM2 similar proteins: A0JXX3, A0QRH1, A1KG35, A1R7J5, A1R990, A4QB40, A4T183, A5TZT8, A9WRT1, B0U3W1, B1MHC3, B2I705, C1A0X5, C1AKN8, O32960, O53176, P0A639, P33119, P64183, P66778, P67233, P73467, P77775, P95125, P9WFR2, P9WFR3, P9WGP6, P9WGP7, P9WGR6, P9WGR7, P9WGS2, P9WGS3, P9WH08, P9WH09, P9WN80, P9WN81, Q07946, Q3AVX2, Q47LE2, Q5HQV8

Diamond homologs: O31574, O32960, P67233, P71373, P73467, P77775, P9WGP6, P9WGP7, Q17QH8, Q2FIM4, Q2G035, Q2YSF6, Q49VZ4, Q4L4J7, Q5HHP9, Q5HQV8, Q5M8N4, Q6GB61, Q6GIM1, Q7A6Q5, Q8CPY7, Q8NXL7, Q99VK8, Q9NRG7, Q9SJU9, P24550, P56985, P56997

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

17 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	12
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

974 predictions. Top by Δscore:

Variant	Effect	Δscore
14:24442340:ACTT:A	donor_loss	1.0000
14:24442341:CTTA:C	donor_loss	1.0000
14:24442342:TTA:T	donor_loss	1.0000
14:24442343:TA:T	donor_loss	1.0000
14:24442344:A:AC	donor_gain	1.0000
14:24442344:AC:A	donor_gain	1.0000
14:24442344:ACC:A	donor_gain	1.0000
14:24442345:C:CT	donor_gain	1.0000
14:24442345:CC:C	donor_gain	1.0000
14:24442345:CCC:C	donor_gain	1.0000
14:24442345:CCCA:C	donor_gain	1.0000
14:24442572:ATCCC:A	donor_gain	1.0000
14:24440390:C:CT	acceptor_gain	0.9900
14:24440390:C:T	acceptor_gain	0.9900
14:24440777:TCTCA:T	donor_loss	0.9900
14:24440779:TCA:T	donor_loss	0.9900
14:24440927:C:CC	acceptor_gain	0.9900
14:24440932:G:T	acceptor_gain	0.9900
14:24441677:CA:C	donor_gain	0.9900
14:24441695:AGG:A	donor_gain	0.9900
14:24442173:CTGA:C	donor_loss	0.9900
14:24442174:TGA:T	donor_loss	0.9900
14:24442175:GACCT:G	donor_loss	0.9900
14:24442176:AC:A	donor_loss	0.9900
14:24442258:ATCCT:A	acceptor_loss	0.9900
14:24442259:TC:T	acceptor_gain	0.9900
14:24442259:TCCTG:T	acceptor_loss	0.9900
14:24442260:CC:C	acceptor_gain	0.9900
14:24442260:CCTGT:C	acceptor_loss	0.9900
14:24442261:C:CA	acceptor_loss	0.9900

AlphaMissense

1854 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:24440789:G:T	R156S	0.982
14:24440440:A:C	F175L	0.980
14:24440440:A:T	F175L	0.980
14:24440442:A:G	F175L	0.980
14:24440840:A:G	W139R	0.980
14:24440840:A:T	W139R	0.980
14:24442213:G:C	N57K	0.980
14:24442213:G:T	N57K	0.980
14:24440317:A:C	N216K	0.977
14:24440317:A:T	N216K	0.977
14:24441695:A:G	W103R	0.977
14:24441695:A:T	W103R	0.977
14:24441794:A:G	W70R	0.977
14:24441794:A:T	W70R	0.977
14:24440391:A:G	W192R	0.975
14:24440391:A:T	W192R	0.975
14:24441758:G:T	R82S	0.974
14:24442380:A:T	V30D	0.974
14:24442436:G:C	F11L	0.973
14:24442436:G:T	F11L	0.973
14:24442438:A:G	F11L	0.973
14:24441792:C:A	W70C	0.972
14:24441792:C:G	W70C	0.972
14:24442432:C:A	G13W	0.972
14:24442346:C:A	W41C	0.969
14:24442346:C:G	W41C	0.969
14:24442431:C:T	G13E	0.968
14:24440281:A:C	F228L	0.965
14:24440281:A:T	F228L	0.965
14:24440283:A:G	F228L	0.965

dbSNP variants (sampled 300 via entrez): RS1001158420 (14:24443539 C>T), RS1001346952 (14:24439385 C>T), RS1001776218 (14:24439794 A>C,G), RS1002455742 (14:24443269 T>C), RS1002558024 (14:24441206 T>A), RS1002562138 (14:24443962 C>A,G,T), RS1002660565 (14:24443852 T>C), RS1002782740 (14:24440901 C>T), RS1004834687 (14:24444539 T>G), RS1004950515 (14:24444767 C>G), RS1006102223 (14:24441372 T>C), RS1006591236 (14:24440180 A>G), RS1007400728 (14:24439843 C>T), RS1008868742 (14:24444554 C>G), RS1009187891 (14:24444490 G>T)

Disease associations

OMIM: gene MIM:616162 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression, decreases expression, affects cotreatment	3
cobaltous chloride	decreases expression	2
Smoke	decreases expression, increases abundance	2
beta-lapachone	decreases expression, increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
bisphenol B	increases expression	1
abrine	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Arsenic Trioxide	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	decreases methylation	1
Carbamazepine	affects expression	1
NADP	affects binding, increases activity	1
Plant Extracts	affects cotreatment, increases expression	1
Tretinoin	affects cotreatment, increases expression	1
Valproic Acid	affects expression	1
Vitamin E	decreases expression	1
Aflatoxin B1	decreases methylation	1
Copper Sulfate	decreases expression	1
Acrylamide	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_TK30	HAP1 SDR39U1 (-)	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.