SLC35D1

Summary

SLC35D1 (solute carrier family 35 member D1, HGNC:20800) is a protein-coding gene on chromosome 1p31.3, encoding Nucleotide sugar transporter SLC35D1 (Q9NTN3). Antiporter that transports nucleotide sugars across the endoplasmic reticulum (ER) membrane in exchange for either their cognate nucleoside monophosphate or another nucleotide sugar.

Glycosylation of cellular glycoconjugates occurs in the endoplasmic reticulum (ER) and Golgi compartment, and requires transport of nucleotide sugars from the cytosol into the lumen of the ER and Golgi by specific transporters. The protein encoded by this gene resides in the ER, and transports both UDP-glucuronic acid (UDP-GlcA) and UDP-N-acetylgalactosamine (UDP-GalNAc) from the cytoplasm to the ER lumen. It may participate in glucuronidation and/or chondroitin sulfate biosynthesis. Mutations in this gene are associated with Schneckenbecken dysplasia.

Source: NCBI Gene 23169 — RefSeq curated summary.

At a glance

• Gene–disease (curated): schneckenbecken dysplasia (Definitive, ClinGen)
• GWAS associations: 16
• Clinical variants (ClinVar): 251 total — 9 pathogenic, 6 likely-pathogenic
• Phenotypes (HPO): 47
• Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
• MANE Select transcript: NM_015139

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20800
Approved symbol	SLC35D1
Name	solute carrier family 35 member D1
Location	1p31.3
Locus type	gene with protein product
Status	Approved
Aliases	UGTREL7, KIAA0260
Ensembl gene	ENSG00000116704
Ensembl biotype	protein_coding
OMIM	610804
Entrez	23169

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000235345, ENST00000901512, ENST00000901513, ENST00000901514

RefSeq mRNA: 1 — MANE Select: NM_015139 NM_015139

CCDS: CCDS636

Canonical transcript exons

ENST00000235345 — 12 exons

Exon	Start	End
ENSE00000774260	67009085	67009167
ENSE00000774261	67020369	67020447
ENSE00000774262	67021535	67021602
ENSE00000774263	67042236	67042328
ENSE00000774264	67047265	67047367
ENSE00000774265	67049782	67049850
ENSE00000774266	67050433	67050504
ENSE00000774267	67052012	67052079
ENSE00000774268	67052771	67052857
ENSE00000774269	67052956	67052989
ENSE00001174421	66999350	67004448
ENSE00001174494	67053811	67054148

Expression profiles

Bgee: expression breadth ubiquitous, 282 present calls, max score 98.20.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.8356 / max 107.7437, expressed in 1710 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
12737	2.4053	1215
12739	2.0779	818
12738	1.9804	1160
12736	0.3720	174

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	98.20	gold quality
mucosa of sigmoid colon	UBERON:0004993	96.70	gold quality
colonic mucosa	UBERON:0000317	96.50	gold quality
oocyte	CL:0000023	96.18	gold quality
jejunal mucosa	UBERON:0000399	96.14	gold quality
tibia	UBERON:0000979	95.67	gold quality
ileal mucosa	UBERON:0000331	94.56	gold quality
liver	UBERON:0002107	93.60	gold quality
skin of hip	UBERON:0001554	91.43	gold quality
jejunum	UBERON:0002115	90.86	gold quality
rectum	UBERON:0001052	90.85	gold quality
right lobe of liver	UBERON:0001114	90.75	gold quality
superficial temporal artery	UBERON:0001614	90.52	gold quality
duodenum	UBERON:0002114	89.89	gold quality
cauda epididymis	UBERON:0004360	89.01	gold quality
gluteal muscle	UBERON:0002000	88.96	gold quality
blood vessel layer	UBERON:0004797	88.93	gold quality
pylorus	UBERON:0001166	88.45	gold quality
hair follicle	UBERON:0002073	88.34	gold quality
caput epididymis	UBERON:0004358	88.34	gold quality
tongue squamous epithelium	UBERON:0006919	88.34	gold quality
mucosa of transverse colon	UBERON:0004991	88.30	gold quality
choroid plexus epithelium	UBERON:0003911	88.24	gold quality
adrenal tissue	UBERON:0018303	88.16	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	88.03	gold quality
corpus epididymis	UBERON:0004359	87.22	gold quality
decidua	UBERON:0002450	87.08	gold quality
nipple	UBERON:0002030	86.81	gold quality
thymus	UBERON:0002370	86.48	gold quality
trabecular bone tissue	UBERON:0002483	85.76	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.29

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

199 targeting SLC35D1, 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-6873-3P	100.00	71.42	2626
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 4)

• Loss of function mutations cause Schneckenbecken dysplasia, a severe skeletal dysplasia. (PMID:17952091)
• Searched for SLC35D1 mutations, identified four novel mutations in three Schneckenbecken dysplasia families. All mutations result in loss of function. No SLC35D1 mutations were id’d in all patients with other spondylodysplastic dysplasias group diseases. (PMID:19508970)
• there is a positive association between the GWAS reported rs3762318 and leprosy, and SLC35D1 and IL23R might be the causal genes (PMID:27712858)
• A novel SLC35D1 variant causing milder phenotype of Schneckenbecken dysplasia in a large pedigree. (PMID:35934917)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc35d1a	ENSDARG00000011973
danio_rerio	slc35d1b	ENSDARG00000027986
mus_musculus	Slc35d1	ENSMUSG00000028521
rattus_norvegicus	Slc35d1	ENSRNOG00000022967

Paralogs (9): SLC35C2 (ENSG00000080189), SLC35E4 (ENSG00000100036), SLC35E1 (ENSG00000127526), SLC35D2 (ENSG00000130958), TMEM241 (ENSG00000134490), SLC35E3 (ENSG00000175782), SLC35C1 (ENSG00000181830), SLC35D3 (ENSG00000182747), SLC35E2B (ENSG00000189339)

Protein

Protein identifiers

Nucleotide sugar transporter SLC35D1 — Q9NTN3 (reviewed: Q9NTN3)

Alternative names: Solute carrier family 35 member D1, UDP-galactose transporter-related protein 7, UDP-glucuronic acid/UDP-N-acetylgalactosamine transporter

All UniProt accessions (1): Q9NTN3

UniProt curated annotations — full annotation on UniProt →

Function. Antiporter that transports nucleotide sugars across the endoplasmic reticulum (ER) membrane in exchange for either their cognate nucleoside monophosphate or another nucleotide sugar. Transports various UDP-sugars including UDP-N-acetyl-alpha-D-glucosamine (UDP-GlcNAc), UDP-N-acetyl-alpha-D-galactosamine (UDP-GalNAc) and UDP-alpha-D-glucuronate (UDP-GlcA), which are used by ER glucosyltransferases as sugar donors for the synthesis of sugar chains of glycoproteins, glycolipids and oligosaccharides. May couple UDP-GlcNAc or UDP-GalNAc efflux to UDP-GlcA influx into the ER lumen that in turn stimulates glucuronidation and subsequent excretion of endobiotics and xenobiotics. Plays a role in chondroitin sulfate biosynthesis, which is important for formation of cartilage extracellular matrix and normal skeletal development.

Subcellular location. Endoplasmic reticulum membrane.

Tissue specificity. Ubiquitous.

Disease relevance. Schneckenbecken dysplasia (SHNKND) [MIM:269250] A rare, lethal autosomal recessive skeletal dysplasia characterized by snail-like configuration of the hypoplastic iliac bone, short-limbed dwarfism, short ribs, and flattened, hypoplastic vertebral bodies. SHNKND is lethal in the neonatal period. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the TPT transporter family. SLC35D subfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NTN3-1	1	yes
Q9NTN3-2	2

RefSeq proteins (1): NP_055954* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004853	Sugar_P_trans_dom	Domain
IPR050186	TPT_transporter	Family

Pfam: PF03151

Catalyzed reactions (Rhea), 10 shown:

• UMP(out) + UDP-N-acetyl-alpha-D-glucosamine(in) = UMP(in) + UDP-N-acetyl-alpha-D-glucosamine(out) (RHEA:72695)
• UMP(out) + UDP-alpha-D-galactose(in) = UMP(in) + UDP-alpha-D-galactose(out) (RHEA:72703)
• UDP-alpha-D-xylose(in) + UMP(out) = UDP-alpha-D-xylose(out) + UMP(in) (RHEA:72723)
• UMP(out) + UDP-alpha-D-glucuronate(in) = UMP(in) + UDP-alpha-D-glucuronate(out) (RHEA:72727)
• UMP(out) + UDP-alpha-D-glucose(in) = UMP(in) + UDP-alpha-D-glucose(out) (RHEA:72731)
• UDP-N-acetyl-alpha-D-galactosamine(in) + UMP(out) = UDP-N-acetyl-alpha-D-galactosamine(out) + UMP(in) (RHEA:72735)
• UDP-N-acetyl-alpha-D-glucosamine(in) + UDP-alpha-D-glucuronate(out) = UDP-N-acetyl-alpha-D-glucosamine(out) + UDP-alpha-D-glucuronate(in) (RHEA:73703)
• UDP-beta-L-arabinopyranose(in) + UMP(out) = UDP-beta-L-arabinopyranose(out) + UMP(in) (RHEA:74671)
• UDP-beta-L-arabinofuranose(in) + UMP(out) = UDP-beta-L-arabinofuranose(out) + UMP(in) (RHEA:74679)
• UDP-N-acetyl-alpha-D-galactosamine(in) + UDP-alpha-D-glucuronate(out) = UDP-N-acetyl-alpha-D-galactosamine(out) + UDP-alpha-D-glucuronate(in) (RHEA:74835)

UniProt features (17 total): transmembrane region 8, sequence variant 4, splice variant 2, chain 1, compositionally biased region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NTN3-F1	80.98	0.35

Function

Pathways and Gene Ontology

Reactome pathways

13 pathways

ID	Pathway
R-HSA-173599	Formation of the active cofactor, UDP-glucuronate
R-HSA-5579020	Defective SLC35D1 causes SCHBCKD
R-HSA-727802	Transport of nucleotide sugars
R-HSA-1430728	Metabolism
R-HSA-156580	Phase II - Conjugation of compounds
R-HSA-156588	Glucuronidation
R-HSA-1643685	Disease
R-HSA-211859	Biological oxidations
R-HSA-382551	Transport of small molecules
R-HSA-425397	Transport of vitamins, nucleosides, and related molecules
R-HSA-425407	SLC-mediated transmembrane transport
R-HSA-5579029	Metabolic disorders of biological oxidation enzymes
R-HSA-5668914	Diseases of metabolism

MSigDB gene sets: 378 (showing top): LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, REACTOME_BIOLOGICAL_OXIDATIONS, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_EMBRYONIC_SKELETAL_SYSTEM_DEVELOPMENT, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, LUCAS_HNF4A_TARGETS_UP, AP2_Q3, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_TRANSPORT, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, GOBP_CHONDROITIN_SULFATE_PROTEOGLYCAN_BIOSYNTHETIC_PROCESS, DOANE_RESPONSE_TO_ANDROGEN_DN, HOSHIDA_LIVER_CANCER_SUBCLASS_S3, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS

GO Biological Process (7): nucleotide-sugar transmembrane transport (GO:0015780), embryonic skeletal system development (GO:0048706), chondroitin sulfate proteoglycan biosynthetic process (GO:0050650), pyrimidine nucleotide-sugar transmembrane transport (GO:0090481), UDP-glucuronate transmembrane transport (GO:0015787), UDP-N-acetylgalactosamine transmembrane transport (GO:0015789), UDP-N-acetylglucosamine transmembrane transport (GO:1990569)

GO Molecular Function (5): UDP-glucuronate transmembrane transporter activity (GO:0005461), UDP-N-acetylglucosamine transmembrane transporter activity (GO:0005462), UDP-N-acetylgalactosamine transmembrane transporter activity (GO:0005463), antiporter activity (GO:0015297), pyrimidine nucleotide-sugar transmembrane transporter activity (GO:0015165)

GO Cellular Component (4): endoplasmic reticulum membrane (GO:0005789), Golgi apparatus (GO:0005794), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-10 pathways:

Category	Pathways
Glucuronidation	1
Metabolic disorders of biological oxidation enzymes	1
Transport of vitamins, nucleosides, and related molecules	1
Biological oxidations	1
Phase II - Conjugation of compounds	1
Metabolism	1
SLC-mediated transmembrane transport	1
Transport of small molecules	1
Diseases of metabolism	1
Disease	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
pyrimidine nucleotide-sugar transmembrane transport	4
pyrimidine nucleotide-sugar transmembrane transporter activity	3
cytoplasm	2
endomembrane system	2
intracellular membrane-bounded organelle	2
organophosphate ester transport	1
nucleobase-containing compound transport	1
transmembrane transport	1
carbohydrate derivative transport	1
skeletal system development	1
chordate embryonic development	1
proteoglycan biosynthetic process	1
chondroitin sulfate proteoglycan metabolic process	1
protein O-linked glycosylation via xylose	1
nucleotide-sugar transmembrane transport	1
carboxylic acid transmembrane transport	1
UDP-glucuronate transmembrane transport	1
carboxylic acid transmembrane transporter activity	1
UDP-N-acetylglucosamine transmembrane transport	1
UDP-N-acetylgalactosamine transmembrane transport	1
secondary active transmembrane transporter activity	1
nucleotide-sugar transmembrane transporter activity	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
cellular anatomical structure	1

Protein interactions and networks

STRING

930 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC35D1	SLC35B1	P78383	950
SLC35D1	SLC35A3	Q9Y2D2	934
SLC35D1	SLC35A1	P78382	928
SLC35D1	SLC35B4	Q969S0	894
SLC35D1	SLC35B2	Q8TB61	874
SLC35D1	SLC35B3	Q9H1N7	841
SLC35D1	MAN2A2	P49641	810
SLC35D1	MAN2A1	Q16706	770
SLC35D1	SLC35A2	P78381	712
SLC35D1	B4GALT1	P15291	706
SLC35D1	SLC35E1	Q96K37	695
SLC35D1	ADGRL1	O94910	677
SLC35D1	SULT4A1	Q9BR01	669
SLC35D1	SLC35H1	Q9NQQ7	651
SLC35D1	SLC35A5	Q9BS91	560

IntAct

0 interactions, top by confidence:

BioGRID (17): SLC35D1 (Affinity Capture-RNA), SLC35D1 (Affinity Capture-MS), SLC35D1 (Negative Genetic), SLC35D1 (Proximity Label-MS), SLC35D1 (Affinity Capture-MS), SLC35D1 (Proximity Label-MS), SLC35D1 (Proximity Label-MS), SLC35D1 (Affinity Capture-RNA), SLC35D1 (Proximity Label-MS), SLC35D1 (Proximity Label-MS), SLC35D1 (Proximity Label-MS), SLC35D1 (Proximity Label-MS), SLC35D1 (Proximity Label-MS), SLC35D1 (Proximity Label-MS), SLC35D1 (Proximity Label-MS)

ESM2 similar proteins: A2AKQ0, A2VE55, A5GFZ5, B8B7Q4, F4JN00, O14494, O42602, O60762, O70152, O75352, O88956, P0CK96, P60588, Q15B89, Q1JQ93, Q28HF8, Q2M3R5, Q3ZCD7, Q4L208, Q4R8V4, Q52KD1, Q5PT50, Q5PT53, Q5RDC9, Q5XF09, Q5ZJ75, Q5ZJH8, Q64232, Q6DBP3, Q6DHK8, Q6NMB6, Q6ZL17, Q762D5, Q76EJ3, Q7T0V6, Q8C811, Q8GUJ1, Q8IVW8, Q8R4D1, Q8RXL8

Diamond homologs: A2AKQ0, A2VE55, A8MRY9, Q15B89, Q18779, Q54YK1, Q5RDC9, Q762D5, Q76EJ3, Q95YI5, Q9NTN3, Q94B65, Q5M8T2, Q8BGF8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	9
Likely pathogenic	6
Uncertain significance	81
Likely benign	89
Benign	46

Top pathogenic / likely-pathogenic (15)

Variant ID	HGVS	Classification
1123	NM_015139.3(SLC35D1):c.125del (p.Lys42fs)	Pathogenic
1125	NM_015139.3(SLC35D1):c.636+1G>T	Pathogenic
1126	NM_015139.3(SLC35D1):c.319C>T (p.Arg107Ter)	Pathogenic
1127	NM_015139.3(SLC35D1):c.392+3A>G	Pathogenic
1128	NM_015139.3(SLC35D1):c.533+730_637-1766del	Pathogenic
1129	NM_015139.3(SLC35D1):c.193A>C (p.Thr65Pro)	Pathogenic
2005679	NM_015139.3(SLC35D1):c.64_70del (p.Thr22fs)	Pathogenic
3691465	NM_015139.3(SLC35D1):c.479G>A (p.Trp160Ter)	Pathogenic
4771008	NM_015139.3(SLC35D1):c.850dup (p.Thr284fs)	Pathogenic
1124	NM_015139.3(SLC35D1):c.932G>A (p.Trp311Ter)	Likely pathogenic
1325087	NM_015139.3(SLC35D1):c.496_497del (p.Val166fs)	Likely pathogenic
1499652	NM_015139.3(SLC35D1):c.464+1G>C	Likely pathogenic
2633725	NM_015139.3(SLC35D1):c.637G>T (p.Glu213Ter)	Likely pathogenic
3075713	NM_015139.3(SLC35D1):c.919T>A (p.Tyr307Asn)	Likely pathogenic
3652026	NM_015139.3(SLC35D1):c.876+1G>A	Likely pathogenic

SpliceAI

1967 predictions. Top by Δscore:

Variant	Effect	Δscore
1:67009164:TATT:T	acceptor_gain	1.0000
1:67020364:CTT:C	donor_loss	1.0000
1:67020365:TTA:T	donor_loss	1.0000
1:67020366:TA:T	donor_loss	1.0000
1:67020444:AAACC:A	acceptor_loss	1.0000
1:67020446:ACC:A	acceptor_loss	1.0000
1:67020447:CCTAG:C	acceptor_loss	1.0000
1:67020448:C:A	acceptor_loss	1.0000
1:67020449:T:G	acceptor_loss	1.0000
1:67021530:CTTAC:C	donor_loss	1.0000
1:67021531:TTA:T	donor_loss	1.0000
1:67021533:A:AG	donor_loss	1.0000
1:67021533:AC:A	donor_gain	1.0000
1:67021533:ACC:A	donor_gain	1.0000
1:67021534:C:CT	donor_loss	1.0000
1:67021534:CC:C	donor_gain	1.0000
1:67021534:CCC:C	donor_gain	1.0000
1:67021599:CAGC:C	acceptor_gain	1.0000
1:67021600:AGCC:A	acceptor_loss	1.0000
1:67021601:GC:G	acceptor_gain	1.0000
1:67021601:GCC:G	acceptor_loss	1.0000
1:67021602:CC:C	acceptor_gain	1.0000
1:67021602:CCTGC:C	acceptor_loss	1.0000
1:67021603:C:CC	acceptor_gain	1.0000
1:67021604:T:G	acceptor_loss	1.0000
1:67042230:TCCTA:T	donor_loss	1.0000
1:67042231:CCTA:C	donor_loss	1.0000
1:67042232:CTA:C	donor_loss	1.0000
1:67042233:TACC:T	donor_loss	1.0000
1:67042234:ACCTT:A	donor_loss	1.0000

AlphaMissense

2296 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:67004436:G:C	S324R	1.000
1:67004436:G:T	S324R	1.000
1:67004438:T:G	S324R	1.000
1:67004440:C:T	G323E	0.999
1:67004441:C:G	G323R	0.999
1:67004441:C:T	G323R	0.999
1:67009097:C:T	G316D	0.999
1:67009098:C:G	G316R	0.999
1:67020417:G:C	C276W	0.999
1:67047305:G:T	A199E	0.999
1:67049788:G:T	A176D	0.999
1:67049800:C:T	G172E	0.999
1:67049801:C:G	G172R	0.999
1:67049801:C:T	G172R	0.999
1:67049809:A:C	M169R	0.999
1:67050480:T:A	R139S	0.999
1:67050480:T:G	R139S	0.999
1:67050481:C:A	R139I	0.999
1:67050481:C:G	R139T	0.999
1:67050484:A:G	L138P	0.999
1:67052026:G:C	S126R	0.999
1:67052026:G:T	S126R	0.999
1:67052028:T:G	S126R	0.999
1:67004441:C:A	G323W	0.998
1:67004448:G:C	S320R	0.998
1:67004448:G:T	S320R	0.998
1:67009086:T:G	S320R	0.998
1:67009090:A:C	N318K	0.998
1:67009090:A:T	N318K	0.998
1:67009105:G:C	N313K	0.998

dbSNP variants (sampled 300 via entrez): RS1000066423 (1:67015459 A>G), RS1000075971 (1:66978183 G>A), RS1000083424 (1:67043321 G>A,T), RS1000087536 (1:66998096 G>A), RS1000135598 (1:66986348 C>A,T), RS1000201020 (1:67023915 T>C), RS1000202906 (1:67055626 C>G), RS1000216118 (1:67042165 C>G,T), RS1000336801 (1:66984718 A>G), RS1000378727 (1:67035940 C>G), RS1000379958 (1:66990588 T>C), RS1000478497 (1:67011574 C>G), RS1000488241 (1:67055304 A>G,T), RS1000500662 (1:67022617 G>A), RS1000507601 (1:66981580 A>G)

Disease associations

OMIM: gene MIM:610804 | disease phenotypes: MIM:269250, MIM:254110

GenCC curated gene-disease

Disease	Classification	Inheritance
schneckenbecken dysplasia	Definitive	Autosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
schneckenbecken dysplasia	Definitive	AR

Mondo (3): schneckenbecken dysplasia (MONDO:0010013), connective tissue disorder (MONDO:0003900), autosomal recessive limb-girdle muscular dystrophy type 2H (MONDO:0009683)

Orphanet (2): Schneckenbecken dysplasia (Orphanet:3144), TRIM32-related limb-girdle muscular dystrophy R8 (Orphanet:1878)

HPO phenotypes

47 total (30 of 47 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000028	Cryptorchidism
HP:0000175	Cleft palate
HP:0000256	Macrocephaly
HP:0000268	Dolichocephaly
HP:0000272	Malar flattening
HP:0000470	Short neck
HP:0000773	Short ribs
HP:0000774	Narrow chest
HP:0000882	Hypoplastic scapulae
HP:0000895	Lateral clavicle hook
HP:0000907	Anterior rib cupping
HP:0000926	Platyspondyly
HP:0000944	Abnormal metaphysis morphology
HP:0000946	Hypoplastic ilia
HP:0000947	Dumbbell-shaped long bone
HP:0001004	Lymphedema
HP:0001156	Brachydactyly
HP:0001231	Abnormal fingernail morphology
HP:0001537	Umbilical hernia
HP:0001538	Protuberant abdomen
HP:0001561	Polyhydramnios
HP:0001776	Bilateral talipes equinovarus
HP:0001790	Nonimmune hydrops fetalis
HP:0001800	Hypoplastic toenails
HP:0002983	Micromelia
HP:0003025	Metaphyseal irregularity
HP:0003026	Short long bone
HP:0003038	Fibular hypoplasia
HP:0003180	Flat acetabular roof

GWAS associations

16 associations (top):

Study	Trait	p-value
GCST001438_1	Crohn’s disease	1.000000e-18
GCST004131_16	Inflammatory bowel disease	5.000000e-111
GCST004132_7	Crohn’s disease	6.000000e-93
GCST004133_2	Ulcerative colitis	4.000000e-41
GCST004627_120	Lymphocyte count	1.000000e-18
GCST004633_134	Neutrophil percentage of white cells	7.000000e-11
GCST006409_19	Allergic rhinitis	5.000000e-06
GCST006479_39	Diverticular disease	4.000000e-06
GCST008062_63	Blood urea nitrogen levels	3.000000e-16
GCST008362_138	Birth weight	5.000000e-08
GCST010989_174	Body size at age 10	2.000000e-08
GCST012011_3	Ventral thalamic nuclei volume	2.000000e-10
GCST012322_2	Triglyceride levels x SSRI defined daily dose interaction in schizophrenia or bipolar disorder	1.000000e-07
GCST90002388_606	Lymphocyte count	4.000000e-42
GCST90002399_41	Neutrophil percentage of white cells	3.000000e-12
GCST90002407_658	White blood cell count	1.000000e-16

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0004587	lymphocyte count
EFO:0007990	neutrophil percentage of leukocytes
EFO:0009959	diverticular disease
EFO:0004344	birth weight
EFO:0009819	comparative body size at age 10, self-reported
EFO:0006935	thalamus volume
EFO:0004530	triglyceride measurement
EFO:0005658	response to selective serotonin reuptake inhibitor

MeSH disease descriptors (3)

Descriptor	Name	Tree numbers
D003240	Connective Tissue Diseases	C17.300
C535897	Limb-girdle muscular dystrophy type 2H (supp.)
C536637	Schneckenbecken dysplasia (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — SLC35 family of nucleotide sugar transporters

CTD chemical–gene interactions

46 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, decreases methylation	3
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	2
Acetaminophen	decreases expression	2
Benzo(a)pyrene	affects methylation, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Cyclosporine	decreases expression	2
testosterone enanthate	affects expression	1
methylmercuric chloride	decreases expression	1
alpha phellandrene	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases methylation	1
trichostatin A	increases expression	1
manganese chloride	increases expression, affects cotreatment, increases abundance	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	decreases expression	1
entinostat	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
nutlin 3	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
jinfukang	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Cacodylic Acid	increases expression	1
Cadmium	increases abundance, increases expression	1
Carbamazepine	affects expression	1
Cisplatin	increases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D4T8	HuH7-SLC35D1-KO-c2	Cancer cell line	Male
CVCL_D4T9	HuH7-SLC35D1-KO-c9	Cancer cell line	Male
CVCL_TN16	HAP1 SLC35D1 (-) 1	Cancer cell line	Male
CVCL_TN17	HAP1 SLC35D1 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT01042158	PHASE4	COMPLETED	A Clinical Trial of Ambrisentan and Tadalafil in Pulmonary Arterial Hypertension Associated With Systemic Sclerosis
NCT03688191	PHASE4	UNKNOWN	Study of Sirolimus in CTD-TP in China
NCT04169100	PHASE4	UNKNOWN	Novel Form of Acquired Long QT Syndrome
NCT04197050	PHASE4	UNKNOWN	Effect of Sacubitril/Valsartan on Reduced Right Ventricular Ejection Fraction in Patients With CTD
NCT04928586	PHASE4	UNKNOWN	Immunosuppressant Combined With Pirfenidone in CTD-ILD
NCT05440240	PHASE4	RECRUITING	Percutaneous Needle Fasciotomy +/- Corticosteroid Injection for Dupuytren’s Contracture
NCT05505409	PHASE4	UNKNOWN	Efficacy and Safety of Pirfenidone in CTD-ILD
NCT06499233	PHASE4	RECRUITING	Efficacy and Safety of Prophylactic Treatment for Pneumocystis Jirovecii Pneumonia in Patients With Autoimmune Inflammatory Rheumatic Disease
NCT00864201	PHASE3	UNKNOWN	A Study to Evaluate the Use of Bosentan in Patients With Exercise Induced Pulmonary Arterial Hypertension Associated With Connective Tissue Disease
NCT01196091	PHASE3	COMPLETED	A Study of LY2127399 in Participants With Systemic Lupus Erythematosus
NCT01205438	PHASE3	COMPLETED	A Study of LY2127399 in Participants With Systemic Lupus Erythematosus
NCT01488708	PHASE3	TERMINATED	On Open-Label Study in Participants With Systemic Lupus Erythematosus
NCT03626688	PHASE3	COMPLETED	A Study Evaluating the Efficacy and Safety of Ralinepag to Improve Treatment Outcomes in PAH Patients
NCT03683186	PHASE3	ENROLLING_BY_INVITATION	A Study Evaluating the Long-Term Efficacy and Safety of Ralinepag in Subjects With PAH Via an Open-Label Extension
NCT04084678	PHASE3	TERMINATED	A Study of Ralinepag to Evaluate Effects on Exercise Capacity by CPET in Subjects With WHO Group 1 PH
NCT06716606	PHASE3	RECRUITING	A Study to Investigate the Long-term Safety and Efficacy of Belimumab in Adults With Interstitial Lung Disease (ILD) Associated With Systemic Sclerosis (SSc) and Other Connective Tissue Diseases (CTD) (BLISSconneCTD-OLE)
NCT06917690	PHASE3	RECRUITING	A Study to Learn About the Safety and Efficacy of the Drug Oleogel-S10 in Japanese Patients With Epidermolysis Bullosa
NCT00004357	PHASE2	COMPLETED	Absorption of Corticosteroids in Children With Juvenile Dermatomyositis
NCT00005675	PHASE2	COMPLETED	Oral Type I Collagen for Relieving Scleroderma
NCT01808196	PHASE2	COMPLETED	Testing Effectiveness of Losartan in Patients With EoE With or Without a CTD
NCT02682511	PHASE2	ACTIVE_NOT_RECRUITING	Oral Ifetroban to Treat Diffuse Cutaneous Systemic Sclerosis (SSc) or SSc-associated Pulmonary Arterial Hypertension
NCT04993885	PHASE2	RECRUITING	Avatrombopag in the Treatment of Adult Immune Thrombocytopenia With Autoantibodies
NCT05516758	PHASE2	TERMINATED	A Study of Peresolimab (LY3462817) in Participants With Moderately-to-Severely Active Rheumatoid Arthritis
NCT05998759	PHASE2	RECRUITING	Telitacicept for the Treatment of Connective Tissue Disease-associated Thrombocytopenia
NCT06104228	PHASE2	RECRUITING	129 Xenon MRI as a Biomarker for Diagnosis and Response to Therapy in Pulmonary Arterial Hypertension (PAH)
NCT01093911	PHASE1	COMPLETED	Safety Study of CDP7657 in Healthy Volunteers and Patients With Systemic Lupus Erythematosus (SLE)
NCT01764594	PHASE1	COMPLETED	Safety Study of CDP7657 in Patients With Systemic Lupus Erythematosus
NCT02392130	PHASE1	COMPLETED	A Clinical Trial to Assess the Potential of LEO 130852A Gel to Reduce Steroid Induced Skin Atrophy on Healthy Skin
NCT03337165	PHASE1	COMPLETED	Autologous Tolerogenic Dendritic Cells for Treatment of Patients With Rheumatoid Arthritis
NCT03929120	PHASE1	COMPLETED	Allogeneic Bone Marrow Mesenchymal Stem Cells for Patients With Interstitial Lung Disease (ILD) & Connective Tissue Disorders (CTD)
NCT01424033	PHASE2/PHASE3	TERMINATED	A Clinical Trial for CTD-ILD Treatment
NCT04915482	PHASE2/PHASE3	UNKNOWN	TPO-RAs Combined With Anti-CD20 Antibody in the Treatment of Adult Immune Thrombocytopenia With Autoantibodies
NCT06574581	PHASE1/PHASE2	RECRUITING	ADSCs Therapy in Patients With CTD-ILD
NCT00001330	Not specified	COMPLETED	Study of Silicone-Associated Connective Tissue Diseases
NCT00001641	Not specified	COMPLETED	Study of Heritable Connective Tissue Disorders
NCT00001978	Not specified	TERMINATED	Determination of Kidney Function
NCT00076830	Not specified	COMPLETED	Evaluation and Treatment of Patients With Connective Tissue Disease
NCT00341679	Not specified	COMPLETED	Studies of the Natural History and Pathogenesis of Autoimmune/Connective Tissue Diseases
NCT00470327	Not specified	RECRUITING	A Study of the Natural Progression of Interstitial Lung Disease (ILD)
NCT00491309	Not specified	UNKNOWN	Exercise and Respiratory Therapy in Patients With Rheumatoid Arthritis / Collagenosis and Pulmonary Hypertension