DISP1
Basic information
Region (hg38): 1:222815022-223005995
Links
Phenotypes
GenCC
Source:
- holoprosencephaly (Supportive), mode of inheritance: AR
- holoprosencephaly (Limited), mode of inheritance: Semidominant
- holoprosencephaly (Limited), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (261 variants)
- not_specified (160 variants)
- DISP1-related_disorder (34 variants)
- Microform_holoprosencephaly (4 variants)
- Lobar_holoprosencephaly (2 variants)
- Holoprosencephaly_sequence (2 variants)
- Holoprosencephaly_10 (1 variants)
- DISP1-related_Holoprosencephaly (1 variants)
- Holoprosencephaly_7 (1 variants)
- See_cases (1 variants)
- Esophageal_atresia (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DISP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001377229.1. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 67 | 74 | ||||
missense | 266 | 22 | 297 | |||
nonsense | 13 | 14 | ||||
start loss | 1 | 1 | ||||
frameshift | 8 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
Total | 0 | 2 | 289 | 89 | 15 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
DISP1 | protein_coding | protein_coding | ENST00000284476 | 7 | 190932 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
8.86e-8 | 1.00 | 125655 | 0 | 93 | 125748 | 0.000370 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.930 | 730 | 804 | 0.908 | 0.0000437 | 10177 |
Missense in Polyphen | 137 | 212.13 | 0.64584 | 2729 | ||
Synonymous | -0.563 | 325 | 312 | 1.04 | 0.0000192 | 2886 |
Loss of Function | 3.87 | 21 | 50.7 | 0.414 | 0.00000266 | 640 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00157 | 0.00157 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.000326 | 0.000326 |
Finnish | 0.0000924 | 0.0000462 |
European (Non-Finnish) | 0.000309 | 0.000299 |
Middle Eastern | 0.000326 | 0.000326 |
South Asian | 0.000502 | 0.000490 |
Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Functions in hedgehog (Hh) signaling. Regulates the release and extracellular accumulation of cholesterol-modified hedgehog proteins and is hence required for effective production of the Hh signal (By similarity). Synergizes with SCUBE2 to cause a increase in SHH secretion (PubMed:22902404). {ECO:0000250|UniProtKB:Q3TDN0, ECO:0000269|PubMed:22902404}.;
- Pathway
- HH-Core;Signaling events mediated by the Hedgehog family
(Consensus)
Recessive Scores
- pRec
- 0.112
Intolerance Scores
- loftool
- 0.0629
- rvis_EVS
- 0.37
- rvis_percentile_EVS
- 74.78
Haploinsufficiency Scores
- pHI
- 0.161
- hipred
- N
- hipred_score
- 0.492
- ghis
- 0.463
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.508
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | Medium | Medium |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Disp1
- Phenotype
- craniofacial phenotype; muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; vision/eye phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; skeleton phenotype; respiratory system phenotype; embryo phenotype;
Zebrafish Information Network
- Gene name
- disp1
- Affected structure
- retinal ganglion cell
- Phenotype tag
- abnormal
- Phenotype quality
- disorganized
Gene ontology
- Biological process
- patched ligand maturation;determination of left/right symmetry;embryonic pattern specification;dorsal/ventral pattern formation;peptide transport;regulation of protein secretion;diaphragm development;protein homotrimerization
- Cellular component
- integral component of membrane;basolateral plasma membrane
- Molecular function
- protein binding;peptide transmembrane transporter activity