GPC4
Basic information
Region (hg38): X:133300103-133415489
Links
Phenotypes
GenCC
Source:
- Keipert syndrome (Moderate), mode of inheritance: XLR
- Keipert syndrome (Definitive), mode of inheritance: XL
- Keipert syndrome (Strong), mode of inheritance: XL
- Keipert syndrome (Strong), mode of inheritance: XL
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Keipert syndrome (Nasodigitoacoustic syndrome) | XL | Audiologic/Otolaryngologic; Cardiovascular | In affected individuals, early recognition and treatment of hearing impairment may improve outcomes, including speech and language development; Individuals have been described with pulmonic stenosis (among other features), and awareness may allow prompt diagnosis and management | Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Musculoskeletal; Neurologic | 30982611 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (47 variants)
- Inborn_genetic_diseases (43 variants)
- Keipert_syndrome (19 variants)
- GPC4-related_disorder (11 variants)
- not_specified (5 variants)
- Distal_shortening_of_limbs (1 variants)
- Craniosynostosis_syndrome (1 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPC4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001448.3. 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 | 7 | |||||
missense | 72 | 83 | ||||
nonsense | 6 | |||||
start loss | 0 | |||||
frameshift | 9 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 8 | 9 | 72 | 16 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
GPC4 | protein_coding | protein_coding | ENST00000370828 | 9 | 115388 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.926 | 0.0739 | 125640 | 3 | 0 | 125643 | 0.0000119 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.66 | 159 | 230 | 0.693 | 0.0000182 | 3706 |
Missense in Polyphen | 40 | 95.762 | 0.4177 | 1585 | ||
Synonymous | 0.552 | 82 | 88.6 | 0.925 | 0.00000726 | 1031 |
Loss of Function | 3.39 | 2 | 17.1 | 0.117 | 0.00000129 | 291 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000365 | 0.0000365 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000246 | 0.0000176 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Cell surface proteoglycan that bears heparan sulfate. May be involved in the development of kidney tubules and of the central nervous system (By similarity). {ECO:0000250}.;
- Pathway
- Wnt signaling pathway - Homo sapiens (human);Wnt Signaling Pathway;Signaling by GPCR;Signal Transduction;Metabolism of fat-soluble vitamins;Metabolism of carbohydrates;A tetrasaccharide linker sequence is required for GAG synthesis;HS-GAG biosynthesis;HS-GAG degradation;Heparan sulfate/heparin (HS-GAG) metabolism;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;Metabolism;Metabolism of vitamins and cofactors;Integrin;Retinoid metabolism and transport;G alpha (i) signalling events;Visual phototransduction;GPCR downstream signalling;Wnt Canonical;Wnt Mammals
(Consensus)
Recessive Scores
- pRec
- 0.160
Intolerance Scores
- loftool
- 0.0928
- rvis_EVS
- -0.07
- rvis_percentile_EVS
- 48.35
Haploinsufficiency Scores
- pHI
- 0.875
- hipred
- Y
- hipred_score
- 0.642
- ghis
- 0.536
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.758
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | High | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Gpc4
- Phenotype
- hematopoietic system phenotype;
Zebrafish Information Network
- Gene name
- gpc4
- Affected structure
- slow muscle cell
- Phenotype tag
- abnormal
- Phenotype quality
- disorganized
Gene ontology
- Biological process
- retinoid metabolic process;glycosaminoglycan biosynthetic process;glycosaminoglycan catabolic process;regulation of signal transduction;Wnt signaling pathway, planar cell polarity pathway;regulation of neurotransmitter receptor localization to postsynaptic specialization membrane;synaptic membrane adhesion;regulation of presynapse assembly
- Cellular component
- nucleus;Golgi lumen;plasma membrane;external side of plasma membrane;lysosomal lumen;collagen-containing extracellular matrix;extracellular exosome;glutamatergic synapse;anchored component of presynaptic membrane
- Molecular function
- coreceptor activity involved in Wnt signaling pathway, planar cell polarity pathway