CRNKL1

Summary

CRNKL1 (crooked neck pre-mRNA splicing factor 1, HGNC:15762) is a protein-coding gene on chromosome 20p11.23, encoding Crooked neck-like protein 1 (Q9BZJ0). Involved in pre-mRNA splicing process. It is a common-essential gene (DepMap: required in 99.6% of cancer cell lines).

The crooked neck (crn) gene of Drosophila is essential for embryogenesis and is thought to be involved in cell cycle progression and pre-mRNA splicing. A protein encoded by this human locus has been found to localize to pre-mRNA splicing complexes in the nucleus and is necessary for pre-mRNA splicing. Alternatively spliced transcript variants have been described.

Source: NCBI Gene 51340 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 93 total — 3 pathogenic
• Phenotypes (HPO): 54
• Cancer dependency (DepMap): dependent in 99.6% of screened cell lines (common-essential)
• MANE Select transcript: NM_001278628

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15762
Approved symbol	CRNKL1
Name	crooked neck pre-mRNA splicing factor 1
Location	20p11.23
Locus type	gene with protein product
Status	Approved
Aliases	CRN, CLF, SYF3, Clf1
Ensembl gene	ENSG00000101343
Ensembl biotype	protein_coding
OMIM	610952
Entrez	51340

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 4 protein_coding, 2 nonsense_mediated_decay, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000377327, ENST00000377340, ENST00000490258, ENST00000490910, ENST00000496549, ENST00000521379, ENST00000536226, ENST00000886215

RefSeq mRNA: 5 — MANE Select: NM_001278628 NM_001278625, NM_001278626, NM_001278627, NM_001278628, NM_016652

CCDS: CCDS33446, CCDS63238, CCDS63239

Canonical transcript exons

ENST00000536226 — 14 exons

Exon	Start	End
ENSE00002244402	20052292	20052466
ENSE00003467775	20040686	20040766
ENSE00003498138	20041566	20041625
ENSE00003505067	20048343	20048501
ENSE00003506384	20045308	20045486
ENSE00003516080	20047765	20047931
ENSE00003521184	20042325	20042516
ENSE00003568575	20050470	20050622
ENSE00003572289	20034368	20036362
ENSE00003587736	20049340	20049431
ENSE00003665574	20039609	20039848
ENSE00003667682	20037323	20037571
ENSE00003678658	20038349	20038450
ENSE00003681278	20043492	20043662

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 95.18.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.1148 / max 358.8404, expressed in 1800 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
186574	24.4617	1795
186573	2.1097	797
186572	0.5073	238
186571	0.0361	12

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	95.18	gold quality
ventricular zone	UBERON:0003053	92.66	gold quality
ganglionic eminence	UBERON:0004023	92.41	gold quality
secondary oocyte	CL:0000655	91.80	gold quality
cortical plate	UBERON:0005343	89.55	gold quality
gastrocnemius	UBERON:0001388	89.00	gold quality
muscle of leg	UBERON:0001383	88.64	gold quality
endothelial cell	CL:0000115	88.37	gold quality
sural nerve	UBERON:0015488	88.37	gold quality
adrenal tissue	UBERON:0018303	87.83	gold quality
choroid plexus epithelium	UBERON:0003911	87.68	gold quality
embryo	UBERON:0000922	87.52	gold quality
granulocyte	CL:0000094	87.31	gold quality
colonic epithelium	UBERON:0000397	86.99	gold quality
hindlimb stylopod muscle	UBERON:0004252	86.74	gold quality
tendon	UBERON:0000043	86.64	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.57	gold quality
muscle organ	UBERON:0001630	86.43	gold quality
rectum	UBERON:0001052	86.30	gold quality
islet of Langerhans	UBERON:0000006	86.18	gold quality
germinal epithelium of ovary	UBERON:0001304	86.16	gold quality
stromal cell of endometrium	CL:0002255	86.04	gold quality
mucosa of transverse colon	UBERON:0004991	85.96	gold quality
bone marrow cell	CL:0002092	85.79	gold quality
tibialis anterior	UBERON:0001385	85.75	gold quality
esophagus mucosa	UBERON:0002469	85.60	gold quality
deltoid	UBERON:0001476	85.53	gold quality
leukocyte	CL:0000738	85.50	gold quality
monocyte	CL:0000576	85.43	gold quality
body of uterus	UBERON:0009853	85.39	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-100618	yes	449.11
E-ANND-3	yes	4.54

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

78 targeting CRNKL1, 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-3163	100.00	77.23	8605
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-636	99.80	69.58	1500
HSA-MIR-577	99.78	69.13	2479
HSA-MIR-548AG	99.77	69.25	1492
HSA-MIR-623	99.76	68.16	1170
HSA-MIR-4679	99.76	69.19	1229
HSA-MIR-6885-3P	99.75	70.36	3187
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-1208	99.70	68.28	1533

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.6% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 2)

• Data show that crooked neck activity appears essential as extracts depleted of hcrn fail to splice pre-mRNA. These and related data support the view that crooked neck is a phylogenetically conserved pre-mRNA splicing factor. (PMID:12084575)
• CRNKL1 Is a Highly Selective Regulator of Intron-Retaining HIV-1 and Cellular mRNAs. (PMID:33468685)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	crnkl1	ENSDARG00000007901
mus_musculus	Crnkl1	ENSMUSG00000001767
rattus_norvegicus	LOC102548514	ENSRNOG00000010587
rattus_norvegicus	Crnkl1	ENSRNOG00000040045
drosophila_melanogaster	crn	FBGN0000377
caenorhabditis_elegans		WBGENE00019762

Paralogs (2): XAB2 (ENSG00000076924), PRPF6 (ENSG00000101161)

Protein

Protein identifiers

Crooked neck-like protein 1 — Q9BZJ0 (reviewed: Q9BZJ0)

Alternative names: Crooked neck homolog

All UniProt accessions (3): Q9BZJ0, A0A0C4DGD7, Q5JY65

UniProt curated annotations — full annotation on UniProt →

Function. Involved in pre-mRNA splicing process. As a component of the minor spliceosome, involved in the splicing of U12-type introns in pre-mRNAs.

Subunit / interactions. Identified in the spliceosome C complex. Present in a spliceosome complex assembled in vitro containing CRNKL1, HPRP8BP and SNRPB2. Component of the minor spliceosome, which splices U12-type introns. Isoform 2 seems to be predominant in the spliceosome complex. Interacts with PPIL2 (via the PPIase cyclophilin-type domain); they may form a trimeric complex with HSP90.

Subcellular location. Nucleus. Nucleus speckle.

Tissue specificity. Widely expressed. Highly expressed in testis. Not detected in brain and lung.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the crooked-neck family.

Isoforms (5)

UniProt ID	Names	Canonical?
Q9BZJ0-1	1, Type-II	yes
Q9BZJ0-2	2, Short
Q9BZJ0-3	3
Q9BZJ0-4	4, Type-III
Q9BZJ0-5	5, type-IV

RefSeq proteins (5): NP_001265554, NP_001265555, NP_001265556, NP_001265557, NP_057736 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003107	HAT	Repeat
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR045075	Syf1-like	Family
IPR055430	HAT_Syf1_CNRKL1_C	Domain

Pfam: PF23231

UniProt features (79 total): helix 34, repeat 17, turn 6, splice variant 5, sequence variant 5, region of interest 3, modified residue 2, sequence conflict 2, strand 2, chain 1, compositionally biased region 1, initiator methionine 1

Structure

Experimental structures (PDB)

31 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
8C6J	ELECTRON MICROSCOPY	2.8
6ID1	ELECTRON MICROSCOPY	2.86
7DVQ	ELECTRON MICROSCOPY	2.89
6ID0	ELECTRON MICROSCOPY	2.9
6ICZ	ELECTRON MICROSCOPY	3
8I0R	ELECTRON MICROSCOPY	3
8I0T	ELECTRON MICROSCOPY	3
8I0V	ELECTRON MICROSCOPY	3
7QTT	ELECTRON MICROSCOPY	3.1
6QDV	ELECTRON MICROSCOPY	3.3
8I0U	ELECTRON MICROSCOPY	3.3
9FMD	ELECTRON MICROSCOPY	3.3
6FF4	ELECTRON MICROSCOPY	3.4
6ZYM	ELECTRON MICROSCOPY	3.4
8I0P	ELECTRON MICROSCOPY	3.4
8I0W	ELECTRON MICROSCOPY	3.4
8RO2	ELECTRON MICROSCOPY	3.5
5XJC	ELECTRON MICROSCOPY	3.6
7W59	ELECTRON MICROSCOPY	3.6
7W5A	ELECTRON MICROSCOPY	3.6
5YZG	ELECTRON MICROSCOPY	4.1
8I0S	ELECTRON MICROSCOPY	4.2
7W5B	ELECTRON MICROSCOPY	4.3
6FF7	ELECTRON MICROSCOPY	4.5
5Z58	ELECTRON MICROSCOPY	4.9
7A5P	ELECTRON MICROSCOPY	5
5Z56	ELECTRON MICROSCOPY	5.1
5MQF	ELECTRON MICROSCOPY	5.9
8CH6	ELECTRON MICROSCOPY	5.9
5Z57	ELECTRON MICROSCOPY	6.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BZJ0-F1	75.87	0.36

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 (2): 503, 2

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-72163	mRNA Splicing - Major Pathway
R-HSA-9918481	Dengue Virus-Host Interactions

MSigDB gene sets: 0 (showing top):

GO Biological Process (5): spliceosomal complex assembly (GO:0000245), mRNA splicing, via spliceosome (GO:0000398), RNA processing (GO:0006396), mRNA processing (GO:0006397), RNA splicing (GO:0008380)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (8): Prp19 complex (GO:0000974), nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), nuclear speck (GO:0016607), U2-type catalytic step 2 spliceosome (GO:0071007), catalytic step 2 spliceosome (GO:0071013), post-mRNA release spliceosomal complex (GO:0071014)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
mRNA Splicing	1
Dengue Virus Infection	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
spliceosomal complex	2
U5 snRNP	2
mRNA splicing, via spliceosome	1
protein-RNA complex assembly	1
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
gene expression	1
RNA biosynthetic process	1
primary metabolic process	1
mRNA metabolic process	1
nucleic acid binding	1
binding	1
protein-containing complex	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
nuclear protein-containing complex	1
ribonucleoprotein complex	1
nuclear ribonucleoprotein granule	1
U2-type spliceosomal complex	1
U2 snRNP	1
U6 snRNP	1
catalytic step 2 spliceosome	1
Prp19 complex	1
catalytic complex	1

Protein interactions and networks

STRING

2793 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CRNKL1	SYF2	O95926	883
CRNKL1	CDC5L	Q99459	824
CRNKL1	ZNF830	Q96NB3	792
CRNKL1	SNW1	Q13573	791
CRNKL1	BCAS2	O75934	740
CRNKL1	AQR	O60306	726
CRNKL1	CDC40	O60508	726
CRNKL1	CWC22	Q9HCG8	715
CRNKL1	CWC15	Q9P013	709
CRNKL1	SNRNP200	O75643	703
CRNKL1	DHX16	O60231	697
CRNKL1	PRCC	Q92733	682
CRNKL1	RBM22	Q9NW64	667
CRNKL1	PRPF19	Q9UMS4	648
CRNKL1	XAB2	Q9HCS7	645

IntAct

172 interactions, top by confidence:

A	B	Type	Score
SNRPF	GEMIN2	psi-mi:“MI:0914”(association)	0.910
PPIE	AQR	psi-mi:“MI:0914”(association)	0.810
PRPF19	AQR	psi-mi:“MI:0914”(association)	0.790
PRPF19	PLRG1	psi-mi:“MI:0914”(association)	0.770
SNRPE	GEMIN2	psi-mi:“MI:0914”(association)	0.770
ISY1	AQR	psi-mi:“MI:0914”(association)	0.740
SYF2	AQR	psi-mi:“MI:0914”(association)	0.730
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
SNRPG	GEMIN2	psi-mi:“MI:0914”(association)	0.710
SNRPB	PRMT5	psi-mi:“MI:0914”(association)	0.670
SNW1	AQR	psi-mi:“MI:0914”(association)	0.650
NCBP1	KPNA3	psi-mi:“MI:0914”(association)	0.640
SF3B1	SAP18	psi-mi:“MI:0914”(association)	0.640
PNN	CASC3	psi-mi:“MI:0914”(association)	0.640
SNRPA1	HTATSF1	psi-mi:“MI:0914”(association)	0.640
DHX8	AHCYL1	psi-mi:“MI:0914”(association)	0.640
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
SNRPA1	U2SURP	psi-mi:“MI:0914”(association)	0.640
CRNKL1	CCDC12	psi-mi:“MI:0915”(physical association)	0.630
CCDC12	CRNKL1	psi-mi:“MI:0915”(physical association)	0.630
CRNKL1	HNRNPC	psi-mi:“MI:0914”(association)	0.610
EFTUD2	SART1	psi-mi:“MI:0914”(association)	0.610
NCBP3	SAP18	psi-mi:“MI:0914”(association)	0.530

BioGRID (263): CRNKL1 (Affinity Capture-MS), CRNKL1 (Affinity Capture-MS), CRNKL1 (Affinity Capture-MS), CRNKL1 (Affinity Capture-MS), CRNKL1 (Affinity Capture-MS), CRNKL1 (Affinity Capture-MS), CRNKL1 (Affinity Capture-MS), CRNKL1 (Affinity Capture-MS), CRNKL1 (Affinity Capture-MS), CRNKL1 (Affinity Capture-MS), CRNKL1 (Affinity Capture-MS), CRNKL1 (Affinity Capture-MS), CRNKL1 (Affinity Capture-MS), CRNKL1 (Affinity Capture-MS), CRNKL1 (Affinity Capture-MS)

ESM2 similar proteins: A1A5S1, A1Z9G2, B3DJT0, B3MIF1, O01422, O74970, O94906, P0CO10, P0CO11, P17886, P25991, P63154, P63155, P87312, Q12309, Q12381, Q15020, Q2KJJ0, Q4KLU2, Q4PB37, Q4WT84, Q4WVF4, Q527H0, Q52DF3, Q54XP4, Q54Z08, Q5B3U7, Q5BDX1, Q5BH69, Q5K654, Q5RCC2, Q5REG1, Q6BSP7, Q6C186, Q6CAR6, Q750X3, Q7SAK5, Q7SGD2, Q7SI58, Q86UA1

Diamond homologs: P0CO10, P0CO11, P17886, P63154, P63155, P87312, Q12309, Q4PB37, Q4WT84, Q527H0, Q54XP4, Q5AED6, Q5BDX1, Q5K654, Q6BSP7, Q6C186, Q6CJK2, Q750X3, Q7SGD2, Q9BZJ0, Q9HF03, Q6FW76, Q12996, Q5RDW9, Q99LI7, Q4KLU2, Q86UA1, Q8K2Z2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 173 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 Splicing	36	31.9×	1e-43
Metabolism of non-coding RNA	6	30.7×	9e-07
Transport of Mature Transcript to Cytoplasm	9	27.6×	9e-10
mRNA Splicing - Major Pathway	58	25.6×	8e-67
Processing of Capped Intron-Containing Pre-mRNA	38	25.2×	7e-42
RNA Polymerase II Transcription Termination	14	24.8×	1e-14
mRNA Splicing - Minor Pathway	13	23.5×	3e-13
mRNA 3’-end processing	14	22.2×	7e-14

GO biological processes:

GO term	Partners	Fold	FDR
U2-type prespliceosome assembly	11	45.2×	7e-14
RNA splicing, via transesterification reactions	9	37.0×	2e-10
negative regulation of mRNA splicing, via spliceosome	7	35.3×	8e-08
spliceosomal snRNP assembly	9	34.4×	4e-10
alternative mRNA splicing, via spliceosome	7	31.0×	2e-07
mRNA splicing, via spliceosome	50	30.1×	9e-59
spliceosomal complex assembly	6	23.8×	1e-05
RNA splicing	29	16.8×	6e-25

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	0
Uncertain significance	65
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
4538465	NM_001278628.2(CRNKL1):c.317G>A (p.Arg106His)	Pathogenic
4538466	NM_001278628.2(CRNKL1):c.316C>T (p.Arg106Cys)	Pathogenic
4538467	NM_001278628.2(CRNKL1):c.418C>G (p.Arg140Gly)	Pathogenic

SpliceAI

2382 predictions. Top by Δscore:

Variant	Effect	Δscore
20:20036358:TCAGA:T	acceptor_gain	1.0000
20:20036359:CAGA:C	acceptor_gain	1.0000
20:20036359:CAGAC:C	acceptor_gain	1.0000
20:20036360:AGA:A	acceptor_gain	1.0000
20:20036361:GA:G	acceptor_gain	1.0000
20:20036363:C:CC	acceptor_gain	1.0000
20:20036366:C:CT	acceptor_gain	1.0000
20:20036367:A:T	acceptor_gain	1.0000
20:20037317:TCTTA:T	donor_loss	1.0000
20:20037318:CTTAC:C	donor_loss	1.0000
20:20037319:TTA:T	donor_loss	1.0000
20:20037320:TAC:T	donor_loss	1.0000
20:20037321:A:AC	donor_gain	1.0000
20:20037321:A:AT	donor_loss	1.0000
20:20037321:AC:A	donor_gain	1.0000
20:20037321:ACC:A	donor_gain	1.0000
20:20037322:C:CC	donor_gain	1.0000
20:20037322:CC:C	donor_gain	1.0000
20:20037322:CCC:C	donor_gain	1.0000
20:20037393:T:C	donor_gain	1.0000
20:20037570:ACC:A	acceptor_loss	1.0000
20:20037571:CC:C	acceptor_loss	1.0000
20:20038345:ATAC:A	donor_loss	1.0000
20:20038346:TAC:T	donor_loss	1.0000
20:20038347:A:AC	donor_gain	1.0000
20:20038348:C:CC	donor_gain	1.0000
20:20038348:C:CG	donor_loss	1.0000
20:20038348:CCT:C	donor_gain	1.0000
20:20038350:TTG:T	donor_gain	1.0000
20:20038446:AGCAC:A	acceptor_gain	1.0000

AlphaMissense

4563 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:20036277:G:T	A822D	1.000
20:20036324:A:C	F806L	1.000
20:20036324:A:T	F806L	1.000
20:20036326:A:G	F806L	1.000
20:20038444:A:G	W679R	1.000
20:20038444:A:T	W679R	1.000
20:20039710:A:G	W643R	1.000
20:20039710:A:T	W643R	1.000
20:20047834:A:G	W346R	1.000
20:20047834:A:T	W346R	1.000
20:20049386:A:G	W245R	1.000
20:20049386:A:T	W245R	1.000
20:20050565:C:G	A198P	1.000
20:20050576:A:G	L194P	1.000
20:20050576:A:T	L194H	1.000
20:20050579:T:G	Q193P	1.000
20:20050585:G:T	A191D	1.000
20:20050591:A:G	I189T	1.000
20:20050591:A:T	I189K	1.000
20:20050593:C:A	Q188H	1.000
20:20050593:C:G	Q188H	1.000
20:20036267:C:A	W825C	0.999
20:20036267:C:G	W825C	0.999
20:20036269:A:G	W825R	0.999
20:20036269:A:T	W825R	0.999
20:20036284:C:G	A820P	0.999
20:20036286:A:G	L819P	0.999
20:20036325:A:C	F806C	0.999
20:20036325:A:G	F806S	0.999
20:20036350:A:G	W798R	0.999

dbSNP variants (sampled 300 via entrez): RS1000188392 (20:20055753 A>G), RS1000380367 (20:20049910 C>T), RS1000415849 (20:20055607 T>C), RS1000642457 (20:20057268 A>T), RS1000823775 (20:20045033 G>A), RS1000852035 (20:20051771 T>G), RS1001124772 (20:20038885 G>A), RS1001357297 (20:20054562 G>A), RS1001409339 (20:20039023 A>T), RS1001467456 (20:20048815 G>A), RS1001495450 (20:20042019 G>A), RS1001789559 (20:20042415 G>A), RS1001789691 (20:20036127 C>CA), RS1001861073 (20:20054438 TACAC>T,TAC), RS1001873653 (20:20054391 C>A)

Disease associations

OMIM: gene MIM:610952 | disease phenotypes: MIM:621436

GenCC curated gene-disease

Mondo (1): microcephaly, progressive, with simplified gyral pattern and cerebellar hypoplasia (MONDO:0980935)

Orphanet (0):

HPO phenotypes

54 total (30 of 54 shown, HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0000098	Tall stature
HP:0000154	Wide mouth
HP:0000286	Epicanthus
HP:0000340	Sloping forehead
HP:0000347	Micrognathia
HP:0000369	Low-set ears
HP:0000400	Macrotia
HP:0000431	Wide nasal bridge
HP:0000455	Broad nasal tip
HP:0000483	Astigmatism
HP:0000486	Strabismus
HP:0000520	Proptosis
HP:0000545	Myopia
HP:0000954	Single transverse palmar crease
HP:0000957	Cafe-au-lait spot
HP:0001141	Severely reduced visual acuity
HP:0001249	Intellectual disability
HP:0001250	Seizure
HP:0001252	Hypotonia
HP:0001272	Cerebellar atrophy
HP:0001274	Agenesis of corpus callosum
HP:0001276	Hypertonia
HP:0001298	Encephalopathy
HP:0001302	Pachygyria
HP:0001320	Cerebellar vermis hypoplasia
HP:0001321	Cerebellar hypoplasia
HP:0001338	Partial agenesis of the corpus callosum
HP:0001339	Lissencephaly
HP:0001347	Hyperreflexia

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
Air Pollutants	affects expression, increases abundance, decreases expression	2
Valproic Acid	affects expression, decreases methylation	2
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	decreases expression	1
nickel sulfate	decreases expression	1
M-VAC protocol	increases response to substance	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
Resveratrol	increases expression, affects cotreatment	1
Temozolomide	increases expression	1
Benzene	increases expression	1
Ozone	affects expression, increases abundance	1
Plant Extracts	affects cotreatment, increases expression	1
Ribonucleotides	affects binding	1
Tobacco Smoke Pollution	increases expression	1
Cyclosporine	decreases expression	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	increases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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