PAX1 (paired box 1)

Gene

• Entrez ID: 5075
• Gene name: Paired box 1
• Gene symbol: PAX1
• Synonyms (NCBI Gene): HUP48, OFC2, OTFCS2
• Chromosome: 20
• Chromosome location: 20p11.22
• Summary: This gene is a member of the paired box (PAX) family of transcription factors. Members of the PAX family typically contain a paired box domain and a paired-type homeodomain. These genes play critical roles during fetal development. This gene plays a role

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs540296842	G>C,T	Pathogenic	Coding sequence variant, missense variant
rs1158294764	C>A,T	Pathogenic	Stop gained, synonymous variant, coding sequence variant
rs1555804780	->GCCCG	Likely-pathogenic	Coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT716300	hsa-miR-646	HITS-CLIP	19536157
MIRT716299	hsa-miR-4660	HITS-CLIP	19536157
MIRT716298	hsa-miR-6828-5p	HITS-CLIP	19536157
MIRT716297	hsa-miR-671-5p	HITS-CLIP	19536157
MIRT716296	hsa-miR-6079	HITS-CLIP	19536157
MIRT643407	hsa-miR-5193	HITS-CLIP	23824327
MIRT643406	hsa-miR-660-3p	HITS-CLIP	23824327
MIRT643405	hsa-miR-3121-5p	HITS-CLIP	23824327
MIRT643404	hsa-miR-3124-3p	HITS-CLIP	23824327
MIRT643403	hsa-miR-9-5p	HITS-CLIP	23824327
MIRT643402	hsa-miR-5087	HITS-CLIP	23824327
MIRT643401	hsa-miR-29b-2-5p	HITS-CLIP	23824327
MIRT643400	hsa-miR-659-3p	HITS-CLIP	23824327
MIRT716300	hsa-miR-646	HITS-CLIP	19536157
MIRT716299	hsa-miR-4660	HITS-CLIP	19536157
MIRT716298	hsa-miR-6828-5p	HITS-CLIP	19536157
MIRT716297	hsa-miR-671-5p	HITS-CLIP	19536157
MIRT716296	hsa-miR-6079	HITS-CLIP	19536157
MIRT643407	hsa-miR-5193	HITS-CLIP	23824327
MIRT643406	hsa-miR-660-3p	HITS-CLIP	23824327
MIRT643405	hsa-miR-3121-5p	HITS-CLIP	23824327
MIRT643404	hsa-miR-3124-3p	HITS-CLIP	23824327
MIRT643403	hsa-miR-9-5p	HITS-CLIP	23824327
MIRT643402	hsa-miR-5087	HITS-CLIP	23824327
MIRT643401	hsa-miR-29b-2-5p	HITS-CLIP	23824327
MIRT643400	hsa-miR-659-3p	HITS-CLIP	23824327
MIRT1215255	hsa-miR-296-3p	CLIP-seq
MIRT1215256	hsa-miR-3613-3p	CLIP-seq
MIRT1215257	hsa-miR-520d-5p	CLIP-seq
MIRT1215258	hsa-miR-524-5p	CLIP-seq
MIRT1215259	hsa-miR-556-3p	CLIP-seq
MIRT2061955	hsa-miR-3119	CLIP-seq
MIRT2061956	hsa-miR-3154	CLIP-seq
MIRT2061957	hsa-miR-384	CLIP-seq
MIRT2061958	hsa-miR-3940-5p	CLIP-seq
MIRT2061959	hsa-miR-4330	CLIP-seq
MIRT2061960	hsa-miR-4436b-5p	CLIP-seq
MIRT2061961	hsa-miR-4507	CLIP-seq
MIRT2061962	hsa-miR-4652-3p	CLIP-seq
MIRT2061963	hsa-miR-539	CLIP-seq
MIRT2061964	hsa-miR-570	CLIP-seq
MIRT2290432	hsa-miR-3130-5p	CLIP-seq
MIRT2290433	hsa-miR-4328	CLIP-seq
MIRT2290434	hsa-miR-4482	CLIP-seq
MIRT2455953	hsa-miR-188-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	ISA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001501	Process	Skeletal system development	IBA
GO:0001501	Process	Skeletal system development	TAS	9671740
GO:0003677	Function	DNA binding	IEA
GO:0005634	Component	Nucleus	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0006366	Process	Transcription by RNA polymerase II	TAS	1358810
GO:0009792	Process	Embryo development ending in birth or egg hatching	IBA
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536

Other IDs

• MIM: 167411
• HGNC: 8615
• e!Ensembl: ENSG00000125813

Protein

• UniProt ID: P15863
• Protein name: Paired box protein Pax-1 (HuP48)
• Protein function: This protein is a transcriptional activator. It may play a role in the formation of segmented structures of the embryo. May play an important role in the normal development of the vertebral column (By similarity).
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00292	PAX	98 → 222		Domain

• Sequence:

  MKFTLGLGSRAWRVSWEGAAAAAAGPGAGGSALRCRAQRVSSPRLGRRGSRLSGALPLCL
  SRGGGGAQALPDCAGPSPGHPGHPGARQLAGPLAMEQTYGEVNQLGGVFVNGRPLPNAIR
  LRIVELAQLGIRPCDISRQLRVSHGCVSKILARYNETGSILPGAIGGSKPRVTTPNVVKH
  IRDYKQGDPGIFAWEIRDRLLADGVCDKYNVPSVSSISRILRNKIGSLAQPGPYEASKQP
  PSQPTLPYNHIYQYPYPSPVSPTGAKMGSHPGVPGTAGHVSIPRSWPSAHSVSNILGIRT
  FMEQTGALAGSEGTAYSPKMEDWAGVNRTAFPATPAVNGLEKPALEADIKYTQSASTLSA
  VGGFLPACAYPASNQHGVYSAPGGGYLAPGPPWPPAQGPPLAPPGAGVAVHGGELAAAMT
  FKHPSREGSLPAPAARPRTPSVAYTDCPSRPRPPRGSSPRTRARRERQADPGAQVCAAAP
  AIGTGRIGGLAEEEASAGPRGARPASPQAQPCLWPDPPHFLYWSGFLGFSELGF

• Sequence length: 534

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Craniofacial microsomia	Likely pathogenic	rs2122139711	RCV001869849	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Otofaciocervical syndrome 2	Pathogenic; Likely pathogenic	rs1985008715, rs1985007962, rs1555804780, rs1158294764, rs540296842	RCV001523891 RCV001523892 RCV000625741 RCV000984533 RCV000074499	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
BRANCHIO-OTO-RENAL SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOLDENHAR SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OTOFACIOCERVICAL SYNDROME	—	CTD, Disgenet, Orphanet CTD, Disgenet, Orphanet CTD, Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OTOFACIOCERVICAL SYNDROME 1	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OTOFACIOCERVICAL SYNDROME 2, WITH T-CELL DEFICIENCY	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PAX1-related disorder	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Abnormal dermatoglyphic pattern	Abnormal dermatoglyphic pattern	HPO_DG			★☆☆☆☆ Found in Text Mining only
Acquired Kyphoscoliosis	Acquired Kyphoscoliosis	BEFREE	28011632		★☆☆☆☆ Found in Text Mining only
Adenocarcinoma	Adenocarcinoma	BEFREE	24407576		★☆☆☆☆ Found in Text Mining only
Alacrima	Alacrima	HPO_DG			★☆☆☆☆ Found in Text Mining only
Androgen-Insensitivity Syndrome	Androgen-Insensitivity Syndrome	BEFREE	29095406, 30572100		★☆☆☆☆ Found in Text Mining only
Benign Neoplasm	Benign Neoplasm	BEFREE	18942711		★☆☆☆☆ Found in Text Mining only
Byzanthine arch palate	High palate	HPO_DG			★☆☆☆☆ Found in Text Mining only
Carcinoma in situ of uterine cervix	Cervical Intraepithelial Neoplasia	BEFREE	20564139, 24844223, 27293491		★☆☆☆☆ Found in Text Mining only
Carcinoma Squamous Cell	Squamous cell carcinoma	Pubtator	27789946, 39304838	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma, Ovarian Epithelial	Ovarian Epithelial carcinoma	BEFREE	18942711, 30636379		★☆☆☆☆ Found in Text Mining only
cervical cancer	Cervical Cancer	BEFREE	20442585, 24844223, 25973053, 26234429, 26552048, 28472814, 30636379, 31235851, 31589957		★☆☆☆☆ Found in Text Mining only
Cervical Intraepithelial Neoplasia	Cervical Intraepithelial Neoplasia	BEFREE	28472814		★☆☆☆☆ Found in Text Mining only
Cervix carcinoma	Cervix carcinoma	BEFREE	20442585, 24844223, 25973053, 26234429, 26552048, 28472814, 30636379, 31235851, 31589957		★☆☆☆☆ Found in Text Mining only
Conductive hearing loss	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital kyphoscoliosis	Congenital kyphoscoliosis	BEFREE	28011632		★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Endometrial Carcinoma	Endometrial carcinoma	BEFREE	30636379		★☆☆☆☆ Found in Text Mining only
Epithelial ovarian cancer	Ovarian cancer	BEFREE	30636379		★☆☆☆☆ Found in Text Mining only
Epithelioma	Epithelioma	BEFREE	31589957		★☆☆☆☆ Found in Text Mining only
Esophageal Squamous Cell Carcinoma	Esophageal squamous cell carcinoma	Pubtator	28241446, 31629253	Associate	★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Head and Neck Neoplasms	Head and neck neoplasm	Pubtator	24786473, 30777857	Associate	★☆☆☆☆ Found in Text Mining only
Hearing Loss, Mixed Conductive-Sensorineural	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intrahepatic Cholangiocarcinoma	Intrahepatic Cholangiocarcinoma	BEFREE	31589957		★☆☆☆☆ Found in Text Mining only
Irido-corneo-trabecular dysgenesis (disorder)	Anterior segment dysgenesis	BEFREE	9302254		★☆☆☆☆ Found in Text Mining only
Jarcho-Levin syndrome	Jarcho-Levin Syndrome	BEFREE	12833407, 7909508		★☆☆☆☆ Found in Text Mining only
Klippel-Feil Syndrome	Klippel Feil syndrome	BEFREE	12774041, 7909508		★☆☆☆☆ Found in Text Mining only
KLIPPEL-FEIL SYNDROME, AUTOSOMAL DOMINANT	Klippel Feil syndrome	BEFREE	12774041		★☆☆☆☆ Found in Text Mining only
Language Development Disorders	Language development disorders	Pubtator	37924468	Associate	★☆☆☆☆ Found in Text Mining only
Lip and Oral Cavity Carcinoma	Lip and Oral Cavity Carcinoma	BEFREE	27865370, 28960639, 29224816		★☆☆☆☆ Found in Text Mining only
Macrocephaly	Macrocephaly	BEFREE	9350820		★☆☆☆☆ Found in Text Mining only
Macrotia	Macrotia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of mouth	Malignant neoplasm of mouth	BEFREE	27865370, 28960639, 29224816		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of ovary	Ovarian cancer	BEFREE	18942711		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	18942711, 20442585, 24786473, 29224816, 30636379, 31629253		★☆☆☆☆ Found in Text Mining only
Malignant tumor of cervix	Cervical Tumor	BEFREE	20442585, 24844223, 25973053, 26234429, 26552048, 28472814, 30636379, 31235851, 31589957		★☆☆☆☆ Found in Text Mining only
Mouth Diseases	Mouth disease	Pubtator	20564139	Stimulate	★☆☆☆☆ Found in Text Mining only
Mouth Diseases	Mouth disease	Pubtator	24799352, 24844223, 26320460, 27789946	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	20442585, 24799352, 25973053, 26234429, 29224816, 30636379		★☆☆☆☆ Found in Text Mining only
Neural Tube Defects	Neural Tube Defect	BEFREE	11175793, 11320527, 16315099, 8863157, 9826722		★☆☆☆☆ Found in Text Mining only
Neural Tube Defects	Neural tube defect	Pubtator	8863157	Associate	★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	BEFREE	9826722		★☆☆☆☆ Found in Text Mining only
Otofaciocervical Syndrome	Otofaciocervical Syndrome	BEFREE	23851939, 28657137, 29681087		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Otofaciocervical Syndrome	Otofaciocervical Syndrome	ORPHANET_DG	23851939		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Otofaciocervical syndrome	Otofaciocervical Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Otofaciocervical Syndrome	Otofaciocervical syndrome	Pubtator	35879406, 37924468	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Otofaciocervical Syndrome	Otofaciocervical Syndrome	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OTOFACIOCERVICAL SYNDROME 1	Otofaciocervical Syndrome	BEFREE	29681087, 31379922		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OTOFACIOCERVICAL SYNDROME 2	Otofaciocervical Syndrome	UNIPROT_DG	23851939		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
OTOFACIOCERVICAL SYNDROME 2	Otofaciocervical Syndrome	BEFREE	29681087		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
OTOFACIOCERVICAL SYNDROME 2	Otofaciocervical Syndrome	CLINVAR_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
ovarian neoplasm	Ovarian neoplasm	BEFREE	18942711		★☆☆☆☆ Found in Text Mining only
Severe Combined Immunodeficiency	Severe combined immunodeficiency disease	BEFREE	28657137		★☆☆☆☆ Found in Text Mining only
Severe Combined Immunodeficiency	Severe combined immunodeficiency	Pubtator	35879406	Associate	★☆☆☆☆ Found in Text Mining only
Sex Differentiation Disorders	Sex Differentiation Disorders	BEFREE	17764081		★☆☆☆☆ Found in Text Mining only
Speech Disorders	Speech Disorders	HPO_DG			★☆☆☆☆ Found in Text Mining only
Spina Bifida	Spina Bifida	BEFREE	8863157, 9826722		★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma	Carcinoma	BEFREE	18398837, 25985991		★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of esophagus	Esophagus Neoplasm	BEFREE	28241446, 31629253		★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	28814981, 30777857	Associate	★☆☆☆☆ Found in Text Mining only
Uterine Cervical Dysplasia	Uterine disease	Pubtator	20442585, 24799352, 27789946	Associate	★☆☆☆☆ Found in Text Mining only
Uterine Cervical Neoplasm	Uterine cervix neoplasm	BEFREE	20833385		★☆☆☆☆ Found in Text Mining only
Uterine Cervical Neoplasms	Uterine neoplasm	Pubtator	20442585, 24844223, 25973053, 25985991, 26552048, 26768780, 27293491, 27789946, 28241446, 31235851, 32616628, 36799003, 37533109, 39304838, 39331483	Associate	★☆☆☆☆ Found in Text Mining only