LSM7

Summary

LSM7 (LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated, HGNC:20470) is a protein-coding gene on chromosome 19p13.3, encoding U6 snRNA-associated Sm-like protein LSm7 (Q9UK45). Plays a role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex). It is a common-essential gene (DepMap: required in 99.8% of cancer cell lines).

Sm-like proteins were identified in a variety of organisms based on sequence homology with the Sm protein family (see SNRPD2; MIM 601061). Sm-like proteins contain the Sm sequence motif, which consists of 2 regions separated by a linker of variable length that folds as a loop. The Sm-like proteins are thought to form a stable heteromer present in tri-snRNP particles, which are important for pre-mRNA splicing.

Source: NCBI Gene 51690 — RefSeq curated summary.

At a glance

• Gene–disease (curated): leukodystrophy (Moderate, GenCC)
• GWAS associations: 1
• Clinical variants (ClinVar): 19 total — 2 pathogenic, 1 likely-pathogenic
• Phenotypes (HPO): 29
• Cancer dependency (DepMap): dependent in 99.8% of screened cell lines (common-essential)
• MANE Select transcript: NM_016199

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20470
Approved symbol	LSM7
Name	LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated
Location	19p13.3
Locus type	gene with protein product
Status	Approved
Aliases	YNL147W
Ensembl gene	ENSG00000130332
Ensembl biotype	protein_coding
OMIM	607287
Entrez	51690

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000252622, ENST00000585395, ENST00000585409, ENST00000587502, ENST00000589532, ENST00000591515, ENST00000591745, ENST00000932498, ENST00000932499

RefSeq mRNA: 1 — MANE Select: NM_016199 NM_016199

CCDS: CCDS45907

Canonical transcript exons

ENST00000252622 — 4 exons

Exon	Start	End
ENSE00000876654	2328387	2328477
ENSE00001623592	2328561	2328586
ENSE00003542372	2324125	2324196
ENSE00003627718	2321521	2321822

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 98.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 31.9422 / max 553.9949, expressed in 1815 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
178162	31.9422	1815

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	98.37	gold quality
granulocyte	CL:0000094	98.32	gold quality
ganglionic eminence	UBERON:0004023	97.82	gold quality
pituitary gland	UBERON:0000007	97.76	gold quality
embryo	UBERON:0000922	97.76	gold quality
ventricular zone	UBERON:0003053	97.70	gold quality
spleen	UBERON:0002106	97.60	gold quality
adenohypophysis	UBERON:0002196	97.60	gold quality
lower esophagus mucosa	UBERON:0035834	97.46	gold quality
monocyte	CL:0000576	97.33	gold quality
cortical plate	UBERON:0005343	97.26	gold quality
small intestine Peyer’s patch	UBERON:0003454	97.25	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	97.23	gold quality
left ovary	UBERON:0002119	97.22	gold quality
mononuclear cell	CL:0000842	97.12	gold quality
lymph node	UBERON:0000029	97.10	gold quality
endocervix	UBERON:0000458	97.10	gold quality
adult organism	UBERON:0007023	97.10	gold quality
leukocyte	CL:0000738	97.07	gold quality
right ovary	UBERON:0002118	96.95	gold quality
ectocervix	UBERON:0012249	96.92	gold quality
transverse colon	UBERON:0001157	96.89	gold quality
right uterine tube	UBERON:0001302	96.73	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	96.67	gold quality
spinal cord	UBERON:0002240	96.60	gold quality
colonic mucosa	UBERON:0000317	96.59	gold quality
mucosa of sigmoid colon	UBERON:0004993	96.57	gold quality
oral cavity	UBERON:0000167	96.51	gold quality
left uterine tube	UBERON:0001303	96.48	gold quality
caudate nucleus	UBERON:0001873	96.46	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-HCAD-4	yes	50.08
E-CURD-122	yes	19.06
E-MTAB-10042	yes	13.51
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting LSM7, 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-570-3P	99.96	72.41	4910
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-1284	99.67	73.56	1353
HSA-MIR-106A-3P	99.53	67.58	995
HSA-MIR-4477A	98.83	69.75	2952
HSA-MIR-4714-3P	96.53	67.44	452

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.8% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 2)

• LSm1-7 proteins colocalize with DCP1,DCP2 and Xrn1 in cytoplasmic foci (PMID:12515382)
• RNA-binding protein LSM7 facilitates breast cancer metastasis through mediating alternative splicing of CD44. (PMID:39182568)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	lsm7	ENSDARG00000058328
mus_musculus	Lsm7	ENSMUSG00000035215
rattus_norvegicus	Lsm7	ENSRNOG00000019552
drosophila_melanogaster	LSm7	FBGN0261068
caenorhabditis_elegans		WBGENE00003081

Paralogs (1): SNRPG (ENSG00000143977)

Protein

Protein identifiers

U6 snRNA-associated Sm-like protein LSm7 — Q9UK45 (reviewed: Q9UK45)

All UniProt accessions (4): Q9UK45, A0A087X2I5, K7EML7, K7ENY5

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex). The heptameric LSM2-8 complex binds specifically to the 3’-terminal U-tract of U6 snRNA.

Subunit / interactions. Component of the precatalytic spliceosome (spliceosome B complex). Component of the U4/U6-U5 tri-snRNP complex, a building block of the precatalytic spliceosome (spliceosome B complex). The U4/U6-U5 tri-snRNP complex is composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39, plus LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8. LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8 form a heptameric, ring-shaped subcomplex (the LSM2-8 complex) that is part of the U4/U6-U5 tri-snRNP complex and the precatalytic spliceosome. Interacts with TACC1.

Subcellular location. Nucleus.

Disease relevance. Leukodystrophy and cerebellar atrophy (LDCA) [MIM:621191] An autosomal recessive disorder characterized by neurodevelopmental features including developmental delay, limited speech, axial hypotonia, and white matter abnormalities with cerebellar atrophy. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the snRNP Sm proteins family.

RefSeq proteins (1): NP_057283* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001163	Sm_dom_euk/arc	Domain
IPR010920	LSM_dom_sf	Homologous_superfamily
IPR017132	Lsm7	Family
IPR044641	Lsm7/SmG-like	Family
IPR047575	Sm	Domain

Pfam: PF01423

UniProt features (7 total): sequence variant 3, initiator methionine 1, chain 1, domain 1, modified residue 1

Structure

Experimental structures (PDB)

20 structures.

PDB	Method	Resolution (Å)
8H6L	ELECTRON MICROSCOPY	2.6
8H6K	ELECTRON MICROSCOPY	2.7
6QW6	ELECTRON MICROSCOPY	2.92
8H6E	ELECTRON MICROSCOPY	3.2
8H6J	ELECTRON MICROSCOPY	3.25
6QX9	ELECTRON MICROSCOPY	3.28
6AHD	ELECTRON MICROSCOPY	3.8
8QZS	ELECTRON MICROSCOPY	4.1
8R09	ELECTRON MICROSCOPY	4.3
8R0B	ELECTRON MICROSCOPY	4.4
5O9Z	ELECTRON MICROSCOPY	4.5
8QO9	ELECTRON MICROSCOPY	5.29
6AH0	ELECTRON MICROSCOPY	5.7
8R0A	ELECTRON MICROSCOPY	5.8
8R08	ELECTRON MICROSCOPY	6.1
8RM5	ELECTRON MICROSCOPY	6.9
3JCR	ELECTRON MICROSCOPY	7
7ABG	ELECTRON MICROSCOPY	7.8
9R8V	ELECTRON MICROSCOPY	8.5
8QXD	ELECTRON MICROSCOPY	9.6

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UK45-F1	89.33	0.70

Functional residue map

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

Post-translational modifications (1): 2

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

ID	Pathway
R-HSA-430039	mRNA decay by 5’ to 3’ exoribonuclease
R-HSA-72163	mRNA Splicing - Major Pathway
R-HSA-429914	Deadenylation-dependent mRNA decay
R-HSA-72172	mRNA Splicing
R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854	Metabolism of RNA

MSigDB gene sets: 179 (showing top): GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, KAAB_FAILED_HEART_ATRIUM_DN, MORF_UBE2I, REACTOME_MRNA_DECAY_BY_5_TO_3_EXORIBONUCLEASE, MORF_HDAC1, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, PUJANA_CHEK2_PCC_NETWORK, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, MUELLER_PLURINET, GOBP_SPLICEOSOMAL_TRI_SNRNP_COMPLEX_ASSEMBLY, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CATABOLIC_PROCESS, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, GNF2_FBL, MORF_BUB3

GO Biological Process (4): mRNA splicing, via spliceosome (GO:0000398), nuclear-transcribed mRNA catabolic process (GO:0000956), mRNA processing (GO:0006397), RNA splicing (GO:0008380)

GO Molecular Function (3): U6 snRNA binding (GO:0017070), RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (14): nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), U6 snRNP (GO:0005688), U12-type spliceosomal complex (GO:0005689), cytosol (GO:0005829), U4/U6 x U5 tri-snRNP complex (GO:0046540), U2-type prespliceosome (GO:0071004), U2-type precatalytic spliceosome (GO:0071005), catalytic step 2 spliceosome (GO:0071013), spliceosomal tri-snRNP complex (GO:0097526), Lsm2-8 complex (GO:0120115), Lsm1-7-Pat1 complex (GO:1990726), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
Metabolism of RNA	2
Deadenylation-dependent mRNA decay	1
mRNA Splicing	1
Processing of Capped Intron-Containing Pre-mRNA	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
cellular anatomical structure	2
spliceosomal snRNP complex	2
spliceosomal complex	2
U5 snRNP	2
U2-type spliceosomal complex	2
U1 snRNP	2
U2 snRNP	2
Sm-like protein family complex	2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
mRNA catabolic process	1
mRNA metabolic process	1
snRNA binding	1
nucleic acid binding	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
nuclear protein-containing complex	1
ribonucleoprotein complex	1
Lsm2-8 complex	1
cytoplasm	1
U4/U6 snRNP	1
spliceosomal tri-snRNP complex	1
prespliceosome	1
U4/U6 x U5 tri-snRNP complex	1
precatalytic spliceosome	1
Prp19 complex	1
catalytic complex	1
protein-containing complex	1

Protein interactions and networks

STRING

2176 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LSM7	LSM1	O15116	998
LSM7	LSM6	P62312	998
LSM7	LSM2	Q9Y333	998
LSM7	LSM5	Q9Y4Y9	997
LSM7	LSM3	P62310	996
LSM7	LSM8	O95777	990
LSM7	LSM4	Q9Y4Z0	988
LSM7	XRN1	Q8IZH2	962
LSM7	SNRPD2	P43330	872
LSM7	TACC1	O75410	763
LSM7	SNRPE	P08578	749
LSM7	SART3	Q15020	671
LSM7	SNRPD3	P43331	667
LSM7	SNRPD1	P13641	667
LSM7	DCP2	Q8IU60	663

IntAct

149 interactions, top by confidence:

A	B	Type	Score
PAIP1	PABPC1	psi-mi:“MI:0914”(association)	0.970
LSM1	LSM3	psi-mi:“MI:0915”(physical association)	0.950
LSM3	LSM1	psi-mi:“MI:0914”(association)	0.950
LSM5	LSM7	psi-mi:“MI:0915”(physical association)	0.900
LSM7	LSM5	psi-mi:“MI:0915”(physical association)	0.900
LSM7	LSM2	psi-mi:“MI:0915”(physical association)	0.900
LSM2	LSM7	psi-mi:“MI:0915”(physical association)	0.900
LSM7	LSM4	psi-mi:“MI:0915”(physical association)	0.890
LSM4	LSM7	psi-mi:“MI:0915”(physical association)	0.890
LSM1	LSM6	psi-mi:“MI:0914”(association)	0.840
LSM6	LSM1	psi-mi:“MI:0914”(association)	0.840
LSM3	LSM7	psi-mi:“MI:0915”(physical association)	0.800
LSM7	LSM6	psi-mi:“MI:0915”(physical association)	0.800
LSM2	LSM8	psi-mi:“MI:0915”(physical association)	0.790
LSM7	DDIT4L	psi-mi:“MI:0915”(physical association)	0.780
DDIT4L	LSM7	psi-mi:“MI:0915”(physical association)	0.780

BioGRID (191): NPY1R (Two-hybrid), LSM7 (Two-hybrid), DDIT4L (Two-hybrid), LSM7 (Two-hybrid), LSM7 (Co-fractionation), LSM7 (Co-fractionation), LSM7 (Co-fractionation), LSM7 (Co-fractionation), LSM7 (Co-fractionation), LSM7 (Co-fractionation), LSM7 (Co-fractionation), LSM7 (Co-fractionation), LSM7 (Co-fractionation), LSM7 (Co-fractionation), LSM7 (Co-fractionation)

ESM2 similar proteins: A2BIG9, A4IGZ4, A6H8I2, B8JKF4, D2GXY4, G2TRR1, O14036, O15116, O74499, O80396, P23059, P47017, P53905, P87173, Q02260, Q06217, Q08DB2, Q0IIM8, Q38E83, Q4R804, Q54HF6, Q54W83, Q55EX5, Q5E9Z8, Q6AZT2, Q6C7U0, Q6DJ48, Q6E0V2, Q6GQ67, Q6NU60, Q6NW58, Q7PWB1, Q8IPZ7, Q8LFL8, Q8N2I9, Q8VC85, Q945P8, Q94C95, Q9BRA0, Q9CQQ8

Diamond homologs: A1XQR9, A4FUI2, A8MWD9, A8XDT0, O26745, O29386, O74966, O82221, P24715, P40204, P47017, P53905, P62303, P62304, P62305, P62308, P62309, P62312, P62313, Q0UWI9, Q0W8R9, Q12U30, Q3ZBL0, Q465S1, Q4PG71, Q54HF6, Q54RX0, Q54W83, Q6BR90, Q8PZZ9, Q8TL47, Q8VYI0, Q945P8, Q9CQQ8, Q9N4G9, Q9SI54, Q9UK45, Q9USZ3, Q9VLV5, Q9VXE0

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
LSM7	“form complex”	“U4/U6.U5 snRNP complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 61 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
mRNA decay by 5’ to 3’ exoribonuclease	6	97.2×	5e-10
Metabolism of non-coding RNA	5	67.5×	2e-07
mRNA Splicing	15	35.0×	5e-18
snRNP Assembly	6	27.0×	2e-06
Processing of Capped Intron-Containing Pre-mRNA	15	26.2×	3e-16
SARS-CoV-2 modulates host translation machinery	5	23.8×	3e-05
mRNA Splicing - Major Pathway	20	23.2×	8e-21
Metabolism of RNA	18	16.0×	4e-16

GO biological processes:

GO term	Partners	Fold	FDR
spliceosomal tri-snRNP complex assembly	6	112.3×	9e-10
spliceosomal snRNP assembly	11	106.5×	3e-18
U2-type prespliceosome assembly	5	52.0×	2e-06
mRNA splicing, via spliceosome	24	36.6×	2e-29
RNA splicing	10	14.7×	1e-07
mRNA processing	8	10.5×	4e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	1
Uncertain significance	9
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
3897536	LSM7, ARG69TRP	Pathogenic
996070	NM_016199.3(LSM7):c.121G>A (p.Asp41Asn)	Pathogenic
996338	NM_016199.3(LSM7):c.206G>C (p.Arg69Pro)	Likely pathogenic

SpliceAI

799 predictions. Top by Δscore:

Variant	Effect	Δscore
19:2321818:AGGGT:A	acceptor_gain	1.0000
19:2321819:GGGT:G	acceptor_gain	1.0000
19:2321820:GGT:G	acceptor_gain	1.0000
19:2321822:TC:T	acceptor_loss	1.0000
19:2321823:C:CA	acceptor_loss	1.0000
19:2321823:C:CC	acceptor_gain	1.0000
19:2324208:C:CT	acceptor_gain	1.0000
19:2324211:C:CT	acceptor_gain	1.0000
19:2324211:C:T	acceptor_gain	1.0000
19:2324212:G:T	acceptor_gain	1.0000
19:2321821:GT:G	acceptor_gain	0.9900
19:2324122:CACCT:C	donor_loss	0.9900
19:2324123:A:AC	donor_gain	0.9900
19:2324124:C:A	donor_loss	0.9900
19:2324124:C:CC	donor_gain	0.9900
19:2324124:CCT:C	donor_gain	0.9900
19:2324124:CCTCG:C	donor_gain	0.9900
19:2324193:CTGG:C	acceptor_gain	0.9900
19:2324198:T:C	acceptor_gain	0.9900
19:2324198:T:TC	acceptor_gain	0.9900
19:2325549:G:T	donor_gain	0.9900
19:2328398:C:A	donor_gain	0.9900
19:2328435:TGG:T	donor_gain	0.9900
19:2324209:A:T	acceptor_gain	0.9800
19:2325168:TGCCA:T	donor_gain	0.9800
19:2328382:CTCA:C	donor_loss	0.9800
19:2328385:ACCTT:A	donor_loss	0.9800
19:2328386:C:G	donor_loss	0.9800
19:2328555:GCTCA:G	donor_loss	0.9800
19:2328556:CTCA:C	donor_loss	0.9800

AlphaMissense

676 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:2321701:G:C	F97L	1.000
19:2321701:G:T	F97L	1.000
19:2321703:A:G	F97L	1.000
19:2321744:A:G	L83P	1.000
19:2321750:A:T	V81E	1.000
19:2321759:C:A	G78V	1.000
19:2321759:C:T	G78D	1.000
19:2321760:C:G	G78R	1.000
19:2321764:G:C	C76W	1.000
19:2321765:C:T	C76Y	1.000
19:2321766:A:G	C76R	1.000
19:2321768:A:T	V75E	1.000
19:2321774:A:G	L73P	1.000
19:2321777:C:A	G72V	1.000
19:2321778:C:G	G72R	1.000
19:2321786:C:G	R69P	1.000
19:2324151:A:G	L48P	1.000
19:2324154:A:T	V47E	1.000
19:2324157:A:G	L46P	1.000
19:2324159:G:C	N45K	1.000
19:2324159:G:T	N45K	1.000
19:2324166:A:G	L43P	1.000
19:2324172:T:A	D41V	1.000
19:2324172:T:C	D41G	1.000
19:2324178:C:T	G39D	1.000
19:2324179:C:A	G39C	1.000
19:2324179:C:G	G39R	1.000
19:2324184:A:G	L37P	1.000
19:2324184:A:T	L37Q	1.000
19:2324190:C:A	G35V	1.000

dbSNP variants (sampled 300 via entrez): RS1000369399 (19:2329144 C>T), RS1000782586 (19:2327427 G>A), RS1000976431 (19:2328321 C>T), RS1001145737 (19:2330101 C>T), RS1001872731 (19:2321875 C>A,T), RS1002056324 (19:2326415 C>T), RS1002121309 (19:2322528 G>A), RS1002783421 (19:2329213 G>A), RS1003097681 (19:2324392 C>T), RS1004125889 (19:2325165 A>G), RS1004331539 (19:2329946 C>G,T), RS1004362089 (19:2323489 T>A,C), RS1004460996 (19:2328118 C>T), RS1004487673 (19:2327932 C>A,G,T), RS1004814901 (19:2323998 GAGA>G)

Disease associations

OMIM: gene MIM:607287 | disease phenotypes: MIM:621191, MIM:312080, MIM:618763

GenCC curated gene-disease

Disease	Classification	Inheritance
leukodystrophy	Moderate	Autosomal recessive

Mondo (3): LSM7-related leukodystrophy and cerebellar atrophy (MONDO:0978294), leukodystrophy (MONDO:0019046), Joubert syndrome 36 (MONDO:0032902)

Orphanet (1): Leukodystrophy (Orphanet:68356)

HPO phenotypes

29 total (29 of 29 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000047	Hypospadias
HP:0000407	Sensorineural hearing impairment
HP:0000486	Strabismus
HP:0000639	Nystagmus
HP:0000739	Anxiety
HP:0000952	Jaundice
HP:0001249	Intellectual disability
HP:0001250	Seizure
HP:0001251	Ataxia
HP:0001257	Spasticity
HP:0001263	Global developmental delay
HP:0001285	Spastic tetraparesis
HP:0001321	Cerebellar hypoplasia
HP:0001337	Tremor
HP:0001622	Premature birth
HP:0002084	Encephalocele
HP:0002098	Respiratory distress
HP:0002172	Postural instability
HP:0002186	Apraxia
HP:0002273	Tetraparesis
HP:0002360	Sleep disturbance
HP:0002415	Leukodystrophy
HP:0007308	Extrapyramidal dyskinesia
HP:0008936	Axial hypotonia
HP:0010865	Oppositional defiant disorder
HP:0010880	Increased nuchal translucency
HP:0011968	Feeding difficulties
HP:0034197	Third trimester onset

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST004902_13	Parkinson’s disease	7.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	3
cobaltous chloride	decreases expression	2
Doxorubicin	decreases expression, affects response to substance	2
bisphenol A	affects expression	1
di-n-butylphosphoric acid	affects expression	1
yessotoxin	decreases expression	1
CGP 52608	affects binding, increases reaction	1
K 7174	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
LDN 193189	affects cotreatment, increases expression	1
PP242	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Irinotecan	increases response to substance	1
Atrazine	decreases expression	1
Coumestrol	increases expression	1
Diazinon	increases methylation	1
Lead	increases expression	1
Smoke	decreases expression	1
Dronabinol	decreases expression	1
Valproic Acid	increases methylation	1
Vinblastine	affects response to substance	1
Vitamin E	decreases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00889174	Not specified	COMPLETED	The Nosology and Etiology of Leukodystrophies of Unknown Causes
NCT01793168	Not specified	RECRUITING	Rare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
NCT02699190	Not specified	COMPLETED	LeukoSEQ: Whole Genome Sequencing as a First-Line Diagnostic Tool for Leukodystrophies
NCT02843555	Not specified	COMPLETED	Natural History of the Leukodystrophies
NCT03047369	Not specified	RECRUITING	The Myelin Disorders Biorepository Project
NCT03333200	Not specified	RECRUITING	Longitudinal Study of Neurodegenerative Disorders
NCT03639285	Not specified	RECRUITING	Natural History, Diagnosis, and Outcomes for Leukodystrophies
NCT05443906	Not specified	RECRUITING	Home Exercise for Individuals with Neurodegenerative Disease