GZF1

Summary

GZF1 (GDNF inducible zinc finger protein 1, HGNC:15808) is a protein-coding gene on chromosome 20p11.21, encoding GDNF-inducible zinc finger protein 1 (Q9H116). Transcriptional repressor that binds the GZF1 responsive element (GRE) (consensus: 5’-TGCGCN[TG][CA]TATA-3’).

Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in nucleolus and nucleoplasm.

Source: NCBI Gene 64412 — RefSeq curated summary.

At a glance

• Gene–disease (curated): Larsen syndrome (Strong, GenCC) — +1 more curated relationship
• Clinical variants (ClinVar): 297 total — 10 pathogenic, 2 likely-pathogenic
• Phenotypes (HPO): 17
• MANE Select transcript: NM_022482

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15808
Approved symbol	GZF1
Name	GDNF inducible zinc finger protein 1
Location	20p11.21
Locus type	gene with protein product
Status	Approved
Aliases	dJ322G13.2, ZBTB23
Ensembl gene	ENSG00000125812
Ensembl biotype	protein_coding
OMIM	613842
Entrez	64412

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 9 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000338121, ENST00000377051, ENST00000424216, ENST00000461789, ENST00000477239, ENST00000907446, ENST00000907447, ENST00000907448, ENST00000907449, ENST00000915629, ENST00000915630

RefSeq mRNA: 3 — MANE Select: NM_022482 NM_001317012, NM_001317019, NM_022482

CCDS: CCDS13151

Canonical transcript exons

ENST00000338121 — 6 exons

Exon	Start	End
ENSE00000859463	23369584	23369741
ENSE00001025751	23362182	23362237
ENSE00001355277	23370091	23373062
ENSE00001472702	23364363	23365747
ENSE00003471644	23367003	23367097
ENSE00003502293	23368762	23368929

Expression profiles

Bgee: expression breadth ubiquitous, 249 present calls, max score 94.36.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.8222 / max 156.7750, expressed in 1749 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
183861	8.8222	1749

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	94.36	gold quality
left ventricle myocardium	UBERON:0006566	92.44	gold quality
endothelial cell	CL:0000115	92.27	gold quality
epithelial cell of pancreas	CL:0000083	90.82	gold quality
middle temporal gyrus	UBERON:0002771	90.30	gold quality
cardiac muscle of right atrium	UBERON:0003379	89.99	silver quality
Brodmann (1909) area 23	UBERON:0013554	89.72	gold quality
tibialis anterior	UBERON:0001385	88.51	silver quality
deltoid	UBERON:0001476	87.99	gold quality
myocardium	UBERON:0002349	87.78	gold quality
heart right ventricle	UBERON:0002080	87.54	gold quality
sural nerve	UBERON:0015488	87.10	gold quality
primary visual cortex	UBERON:0002436	86.94	gold quality
parietal pleura	UBERON:0002400	86.78	gold quality
tibia	UBERON:0000979	86.42	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.04	gold quality
popliteal artery	UBERON:0002250	85.62	gold quality
tibial artery	UBERON:0007610	85.57	gold quality
secondary oocyte	CL:0000655	85.29	gold quality
visceral pleura	UBERON:0002401	85.26	gold quality
right adrenal gland	UBERON:0001233	84.99	gold quality
monocyte	CL:0000576	84.88	gold quality
prefrontal cortex	UBERON:0000451	84.53	gold quality
right adrenal gland cortex	UBERON:0035827	84.44	gold quality
leukocyte	CL:0000738	84.27	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	84.21	gold quality
germinal epithelium of ovary	UBERON:0001304	84.09	gold quality
hindlimb stylopod muscle	UBERON:0004252	84.05	gold quality
left adrenal gland cortex	UBERON:0035825	84.05	gold quality
adrenal gland	UBERON:0002369	83.94	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.31

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
HOXA10	Repression

miRNA regulators (miRDB)

103 targeting GZF1, 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-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-221-5P	99.86	65.45	1052

Literature-anchored findings (GeneRIF, showing 5)

• induction of GZF1 expression via the is required for renal branching morphogenesis (PMID:14522971)
• The repressive activity of GZF1 is modulated by the level at which nucleolin is expressed. (PMID:17674968)
• These findings suggest that GZF1 represents a new marker for renal proximal tubules. (PMID:21292309)
• We report an autosomal-recessive Larsen syndrome that is most likely caused by GZF1 mutations. (PMID:28475863)
• Novel GZF1 pathogenic variants identified in two Chinese patients with Larsen syndrome. (PMID:33009817)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Gzf1	ENSMUSG00000027439
rattus_norvegicus	Gzf1	ENSRNOG00000004735

Paralogs (51): WIZ (ENSG00000011451), ZNF416 (ENSG00000083817), MYNN (ENSG00000085274), PRDM4 (ENSG00000110851), PRDM2 (ENSG00000116731), ZBTB17 (ENSG00000116809), ZNF644 (ENSG00000122482), ZNF426 (ENSG00000130818), ZNF287 (ENSG00000141040), ZNF697 (ENSG00000143067), ZNF687 (ENSG00000143373), ZNF214 (ENSG00000149050), ZNF547 (ENSG00000152433), ZNF776 (ENSG00000152443), ZNF230 (ENSG00000159882), ZNF222 (ENSG00000159885), ZNF233 (ENSG00000159915), ZNF333 (ENSG00000160961), ZNF319 (ENSG00000166188), ZNF592 (ENSG00000166716), ZNF646 (ENSG00000167395), ZNF507 (ENSG00000168813), ZNF768 (ENSG00000169957), ZNF417 (ENSG00000173480), ZNF408 (ENSG00000175213), ZBTB41 (ENSG00000177888), ZNF223 (ENSG00000178386), ZNF852 (ENSG00000178917), ZNF784 (ENSG00000179922), ZNF572 (ENSG00000180938), ZNF707 (ENSG00000181135), ZNF746 (ENSG00000181220), ZNF467 (ENSG00000181444), ZNF530 (ENSG00000183647), ZNF17 (ENSG00000186272), ZNF527 (ENSG00000189164), ZKSCAN7 (ENSG00000196345), ZNF34 (ENSG00000196378), ZNF774 (ENSG00000196391), ZNF777 (ENSG00000196453)

Protein

Protein identifiers

GDNF-inducible zinc finger protein 1 — Q9H116 (reviewed: Q9H116)

Alternative names: Zinc finger and BTB domain-containing protein 23, Zinc finger protein 336

All UniProt accessions (2): Q9H116, Q5JXG1

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional repressor that binds the GZF1 responsive element (GRE) (consensus: 5’-TGCGCN[TG][CA]TATA-3’). May be regulating VSX2/HOX10 expression.

Subunit / interactions. Interacts with NCL.

Subcellular location. Cytoplasm. Nucleus. Nucleoplasm. Nucleolus.

Tissue specificity. Expressed in adult brain, heart, skeletal muscle, kidney and liver. Also detected in fetal brain and kidney, and at lower levels in fetal lung and liver.

Disease relevance. Joint laxity, short stature, and myopia (JLSM) [MIM:617662] An autosomal recessive disease characterized by generalized joint laxity, joint dislocation, pectus carinatum, short stature, and severe myopia with retinal detachment. The disease is caused by variants affecting the gene represented in this entry.

Induction. By GDNF.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9H116-1	1	yes
Q9H116-4	2

RefSeq proteins (3): NP_001303941, NP_001303948, NP_071927* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000210	BTB/POZ_dom	Domain
IPR011333	SKP1/BTB/POZ_sf	Homologous_superfamily
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096, PF00651, PF13894, PF13912

UniProt features (35 total): zinc finger region 10, sequence variant 8, compositionally biased region 5, sequence conflict 4, region of interest 2, mutagenesis site 2, chain 1, domain 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H116-F1	60.05	0.01

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): 613

Mutagenesis-validated functional residues (2):

Position	Phenotype
32	decreased repression activity.
50	decreased repression activity.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 185 (showing top): GOBP_MORPHOGENESIS_OF_AN_EPITHELIUM, GCM_MAP4K4, GOBP_EPITHELIUM_DEVELOPMENT, GCM_PTPRD, GOBP_KIDNEY_EPITHELIUM_DEVELOPMENT, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_NEPHRON_EPITHELIUM_DEVELOPMENT, GROSS_HYPOXIA_VIA_ELK3_DN, GOBP_RENAL_TUBULE_DEVELOPMENT, GROSS_HYPOXIA_VIA_HIF1A_DN, GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_UP, GOBP_MESONEPHRIC_TUBULE_MORPHOGENESIS, SUH_COEXPRESSED_WITH_ID1_AND_ID2_UP, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER

GO Biological Process (4): negative regulation of transcription by RNA polymerase II (GO:0000122), branching involved in ureteric bud morphogenesis (GO:0001658), regulation of DNA-templated transcription (GO:0006355), negative regulation of DNA-templated transcription (GO:0045892)

GO Molecular Function (8): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), zinc ion binding (GO:0008270), sequence-specific DNA binding (GO:0043565), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (4): nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytoplasm (GO:0005737), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA polymerase II transcription regulatory region sequence-specific DNA binding	3
regulation of transcription by RNA polymerase II	2
DNA-templated transcription	2
nuclear lumen	2
cellular anatomical structure	2
transcription by RNA polymerase II	1
negative regulation of DNA-templated transcription	1
branching morphogenesis of an epithelial tube	1
ureteric bud morphogenesis	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
regulation of DNA-templated transcription	1
negative regulation of RNA biosynthetic process	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
negative regulation of transcription by RNA polymerase II	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription repressor activity	1
transition metal ion binding	1
DNA binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membraneless organelle	1
intracellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

898 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GZF1	CST9L	Q9H4G1	531
GZF1	CSTL1	Q9H114	512
GZF1	NXT1	Q9UKK6	502
GZF1	KIZ	Q2M2Z5	473
GZF1	CST8	O60676	456
GZF1	CST11	Q9H112	452
GZF1	CST1	P01037	438
GZF1	CFAP61	Q8NHU2	409
GZF1	RNF166	Q96A37	403
GZF1	KAT14	Q9H8E8	402
GZF1	DTWD1	Q8N5C7	395
GZF1	CFAP68	Q9H5F2	393
GZF1	ACSS1	Q9NUB1	391
GZF1	SACK1F	Q8NEG4	390
GZF1	PPARG	P37231	387

IntAct

88 interactions, top by confidence:

A	B	Type	Score
RPL14	RRP8	psi-mi:“MI:0914”(association)	0.640
RPL30	RRP8	psi-mi:“MI:0914”(association)	0.530
ZBTB48	ZBTB24	psi-mi:“MI:0914”(association)	0.530
RPL7	ZBTB24	psi-mi:“MI:0914”(association)	0.530
E4F1	ZBTB24	psi-mi:“MI:0914”(association)	0.530
RPS3	ZNF316	psi-mi:“MI:0914”(association)	0.530
ZNF169	ZNF316	psi-mi:“MI:0914”(association)	0.530
H1-6	ZNF724	psi-mi:“MI:0914”(association)	0.530
ZC3HAV1	KHNYN	psi-mi:“MI:0914”(association)	0.530
PPAN	PPM1G	psi-mi:“MI:0914”(association)	0.530
H2AC20	PPM1G	psi-mi:“MI:0914”(association)	0.530
ZNF71	NVL	psi-mi:“MI:0914”(association)	0.530
RRP8	NVL	psi-mi:“MI:0914”(association)	0.530
RPL18A	RRP8	psi-mi:“MI:0914”(association)	0.530
RPL8	ZBTB24	psi-mi:“MI:0914”(association)	0.530
RPSA	RPS17	psi-mi:“MI:0914”(association)	0.530
ADARB1	SPTY2D1	psi-mi:“MI:0914”(association)	0.530
MAGEB2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
RPL13	RRP8	psi-mi:“MI:0914”(association)	0.530
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
PPAN	IGF2BP3	psi-mi:“MI:0914”(association)	0.350
GPATCH4	NOP56	psi-mi:“MI:0914”(association)	0.350
rl3_rl3l_human	MPHOSPH10	psi-mi:“MI:0914”(association)	0.350
RPL27A	ZNF320	psi-mi:“MI:0914”(association)	0.350

BioGRID (91): GZF1 (Affinity Capture-MS), GZF1 (Affinity Capture-MS), GZF1 (Affinity Capture-MS), GZF1 (Affinity Capture-MS), GZF1 (Affinity Capture-MS), GZF1 (Affinity Capture-MS), GZF1 (Affinity Capture-MS), GZF1 (Affinity Capture-MS), GZF1 (Affinity Capture-MS), GZF1 (Affinity Capture-MS), GZF1 (Affinity Capture-MS), GZF1 (Affinity Capture-MS), GZF1 (Reconstituted Complex), GZF1 (Affinity Capture-MS), GZF1 (Proximity Label-MS)

ESM2 similar proteins: A0A1D5NS60, A0JN76, A1L2U9, B1WAZ8, E9Q3T6, O15060, O15062, O35260, O93567, P41182, P41183, Q05516, Q0IH98, Q0IJ29, Q0P4X6, Q0V8G8, Q1L8W0, Q3B725, Q3B7N9, Q3SWU4, Q5EAC5, Q5EXX3, Q5R5N5, Q5SW75, Q5ZM39, Q6DDV0, Q6NRK3, Q6NRM8, Q6ZSB9, Q7TQG0, Q7TS63, Q7TSZ8, Q7ZWZ4, Q801P1, Q80X44, Q86VK4, Q8BKX7, Q8BXX2, Q8CII0, Q8NAP3

Diamond homologs: A0A2R8Q1W5, A9JRD8, B0WWP2, B3DIV9, B3M9V8, B3NDN0, B4GRJ2, B4HIK1, B4J045, B4L0G9, B4LIG6, B4MXW3, B4PD06, B4QLQ2, D3Z8N4, D3ZUU2, E0CZ16, E1B932, E7F6F9, E9Q4F2, F1LZ52, F1LZF0, F1MBP6, G3X9X1, O15062, O93567, O94889, O95198, P28575, P57790, Q04652, Q08DK3, Q13105, Q14145, Q16RL8, Q1ECZ2, Q2M0J9, Q2TBA0, Q3SWU4, Q3ZB90

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 91 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
Peptide chain elongation	24	52.5×	1e-34
Viral mRNA Translation	24	52.5×	1e-34
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	24	51.9×	1e-34
Selenocysteine synthesis	24	49.7×	2e-34
Eukaryotic Translation Termination	24	49.7×	2e-34
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	24	48.7×	3e-34
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA	24	48.7×	3e-34
Formation of a pool of free 40S subunits	24	46.3×	8e-34

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	25	54.5×	3e-35
ribosomal large subunit biogenesis	8	41.7×	1e-09
translation	23	27.8×	4e-25
ribosomal small subunit biogenesis	8	21.4×	2e-07
rRNA processing	11	18.3×	2e-09
negative regulation of translation	5	11.5×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	10
Likely pathogenic	2
Uncertain significance	153
Likely benign	101
Benign	23

Top pathogenic / likely-pathogenic (12)

Variant ID	HGVS	Classification
1069491	NM_022482.5(GZF1):c.684_687del (p.Lys230fs)	Pathogenic
1405705	NM_022482.5(GZF1):c.434_435del (p.Glu145fs)	Pathogenic
1421934	NM_022482.5(GZF1):c.510del (p.Asp170fs)	Pathogenic
1687462	NM_022482.5(GZF1):c.1451_1452del (p.Cys484fs)	Pathogenic
1687511	NM_022482.5(GZF1):c.1440del (p.His481fs)	Pathogenic
2697389	NM_022482.5(GZF1):c.1236C>A (p.Cys412Ter)	Pathogenic
2841879	NM_022482.5(GZF1):c.49del (p.Leu17fs)	Pathogenic
438348	NM_022482.5(GZF1):c.865G>T (p.Glu289Ter)	Pathogenic
438349	NM_022482.5(GZF1):c.1054dup (p.Thr352fs)	Pathogenic
4712846	NM_022482.5(GZF1):c.432dup (p.Glu145fs)	Pathogenic
3775591	NM_022482.5(GZF1):c.1647_1648del (p.Cys549_Asp550delinsTer)	Likely pathogenic
548966	GRCh37/hg19 20p11.22-11.21(chr20:21680345-24383453)x1	Likely pathogenic

SpliceAI

1197 predictions. Top by Δscore:

Variant	Effect	Δscore
20:23362238:G:A	donor_loss	1.0000
20:23362239:T:G	donor_loss	1.0000
20:23364359:A:AG	acceptor_gain	1.0000
20:23364360:A:G	acceptor_gain	1.0000
20:23364362:GCT:G	acceptor_gain	1.0000
20:23368757:TGTAG:T	acceptor_loss	1.0000
20:23368758:GTA:G	acceptor_loss	1.0000
20:23368759:TAG:T	acceptor_loss	1.0000
20:23368760:A:C	acceptor_loss	1.0000
20:23369580:TCAG:T	acceptor_loss	1.0000
20:23369582:A:AC	acceptor_loss	1.0000
20:23369582:AG:A	acceptor_gain	1.0000
20:23369582:AGG:A	acceptor_gain	1.0000
20:23369582:AGGG:A	acceptor_gain	1.0000
20:23369583:GG:G	acceptor_gain	1.0000
20:23369583:GGG:G	acceptor_gain	1.0000
20:23369583:GGGG:G	acceptor_gain	1.0000
20:23369583:GGGGA:G	acceptor_gain	1.0000
20:23369742:G:GG	donor_gain	1.0000
20:23370089:A:AG	acceptor_gain	1.0000
20:23370090:G:GG	acceptor_gain	1.0000
20:23362233:GGGAG:G	donor_gain	0.9900
20:23362234:GGAG:G	donor_gain	0.9900
20:23362234:GGAGG:G	donor_gain	0.9900
20:23362235:GAG:G	donor_gain	0.9900
20:23362235:GAGG:G	donor_gain	0.9900
20:23362238:G:GG	donor_gain	0.9900
20:23364358:CAAA:C	acceptor_loss	0.9900
20:23364358:CAAAG:C	acceptor_gain	0.9900
20:23364359:AAAGC:A	acceptor_gain	0.9900

AlphaMissense

4737 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:23365452:T:C	F357L	1.000
20:23365454:C:A	F357L	1.000
20:23365454:C:G	F357L	1.000
20:23367052:T:C	F472L	1.000
20:23367054:C:A	F472L	1.000
20:23367054:C:G	F472L	1.000
20:23368779:T:C	C493R	1.000
20:23368800:T:C	F500L	1.000
20:23368802:T:A	F500L	1.000
20:23368802:T:G	F500L	1.000
20:23368884:T:C	F528L	1.000
20:23368886:T:A	F528L	1.000
20:23368886:T:G	F528L	1.000
20:23369622:T:C	F556L	1.000
20:23369623:T:C	F556S	1.000
20:23369624:C:A	F556L	1.000
20:23369624:C:G	F556L	1.000
20:23369706:T:C	F584L	1.000
20:23369708:C:A	F584L	1.000
20:23369708:C:G	F584L	1.000
20:23365359:T:C	F326L	0.999
20:23365361:T:A	F326L	0.999
20:23365361:T:G	F326L	0.999
20:23365431:T:C	C350R	0.999
20:23365453:T:C	F357S	0.999
20:23365471:T:C	L363P	0.999
20:23365479:C:G	H366D	0.999
20:23365481:C:A	H366Q	0.999
20:23365481:C:G	H366Q	0.999
20:23365518:T:C	C379R	0.999

dbSNP variants (sampled 300 via entrez): RS1000080822 (20:23372929 T>C), RS1000133114 (20:23372742 G>T), RS1000252088 (20:23367511 T>C), RS1000347229 (20:23367972 C>A), RS1000807141 (20:23361557 C>T), RS1000980436 (20:23361227 A>C), RS1001259528 (20:23365838 A>C,G), RS1001354338 (20:23366084 T>C), RS1001748057 (20:23371706 A>G,T), RS1001798909 (20:23371467 C>A,T), RS1002080294 (20:23370118 T>C), RS1002137371 (20:23369874 C>T), RS1002266853 (20:23364062 C>A,G,T), RS1002426026 (20:23359252 C>G), RS1002559255 (20:23371026 C>G)

Disease associations

OMIM: gene MIM:613842 | disease phenotypes: MIM:617662, MIM:150250

GenCC curated gene-disease

Disease	Classification	Inheritance
Larsen syndrome	Strong	Autosomal recessive
joint laxity, short stature, and myopia	Strong	Autosomal recessive

Mondo (2): joint laxity, short stature, and myopia (MONDO:0060556), Larsen syndrome (MONDO:0007875)

Orphanet (2): Severe myopia-generalized joint laxity-short stature syndrome (Orphanet:527450), Larsen syndrome (Orphanet:503)

HPO phenotypes

17 total (17 of 17 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000023	Inguinal hernia
HP:0000365	Hearing impairment
HP:0000501	Glaucoma
HP:0000541	Retinal detachment
HP:0000567	Chorioretinal coloboma
HP:0000612	Iris coloboma
HP:0000768	Pectus carinatum
HP:0001249	Intellectual disability
HP:0001382	Joint hypermobility
HP:0001537	Umbilical hernia
HP:0001762	Talipes equinovarus
HP:0002751	Kyphoscoliosis
HP:0002947	Cervical kyphosis
HP:0004322	Short stature
HP:0011003	High myopia
HP:0012095	Multiple joint dislocation

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C580241	Larsen Syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases expression	3
sodium arsenite	decreases expression, increases expression	2
Acetaminophen	increases expression, decreases expression	2
Air Pollutants	affects expression, increases abundance, decreases expression	2
Benzo(a)pyrene	decreases methylation, increases expression	2
Aflatoxin B1	decreases methylation	2
Cadmium Chloride	decreases expression, increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
FR900359	affects phosphorylation	1
butyraldehyde	decreases expression	1
nickel sulfate	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	increases reaction, affects binding	1
K 7174	increases expression	1
PCI 5002	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Leflunomide	increases expression	1
Caffeine	affects phosphorylation	1
Cisplatin	increases expression	1
Formaldehyde	increases expression	1
Hydrogen Peroxide	affects expression	1
Ozone	affects expression, increases abundance	1
Silver	increases expression	1
Smoke	decreases expression	1
Dronabinol	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Urethane	increases expression	1
Zinc	affects cotreatment, increases expression	1
Cyclosporine	increases expression	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT05052554	PHASE1	WITHDRAWN	Study With QR-504a to Evaluate Safety, Tolerability & Corneal Endothelium Molecular Biomarker(s) in Subjects With FECD3