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VACTERL-like phenotypes v1.34 CDX2 Arina Puzriakova Publications for gene: CDX2 were set to PMID: 34671974
VACTERL-like phenotypes v1.33 CDX2 Arina Puzriakova Classified gene: CDX2 as Green List (high evidence)
VACTERL-like phenotypes v1.33 CDX2 Arina Puzriakova Added comment: Comment on list classification: New gene added by Dmitrijs Rots (RadboudUMC). At least 8 unrelated families reported with de novo or inherited pathogenic variants in CDX2. Phenotypic findings comprise a broad spectrum of caudal abnormalities including defects of the uro‐recto‐genital tract, vertebrae, and the limbs. Cdx2 mutant mice show a variable phenotype that is comparable to that of patients (including imperforate anus, sirenomelia, posterior vertebral truncations, and bladder anomalies).

Overall there is sufficient evidence to promote this gene to Green as the clinical phenotype in some patients shows overlap with VACTERL.
VACTERL-like phenotypes v1.33 CDX2 Arina Puzriakova Gene: cdx2 has been classified as Green List (High Evidence).
VACTERL-like phenotypes v1.32 TRAP1 Eleanor Williams Tag gene-checked tag was added to gene: TRAP1.
VACTERL-like phenotypes v1.32 CDX2 Dmitrijs Rots gene: CDX2 was added
gene: CDX2 was added to VACTERL-like phenotypes. Sources: Literature
Mode of inheritance for gene: CDX2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: CDX2 were set to PMID: 34671974
Phenotypes for gene: CDX2 were set to Multiple congenital anomalies
Penetrance for gene: CDX2 were set to unknown
Review for gene: CDX2 was set to GREEN
Added comment: Multiple patients reported and summarized in PMID: 34671974 with multiple congenital anomalies, including patients with VACTERL-like phenotype.
Sources: Literature
VACTERL-like phenotypes v1.32 WBP11 Ivone Leong Phenotypes for gene: WBP11 were changed from malformation syndrome affecting the cardiac, skeletal, gastrointestinal and renal systems to Vertebral, cardiac, tracheoesophageal, renal, and limb defects, OMIM:619227
VACTERL-like phenotypes v1.31 PLVAP Ivone Leong Classified gene: PLVAP as Green List (high evidence)
VACTERL-like phenotypes v1.31 PLVAP Ivone Leong Gene: plvap has been classified as Green List (High Evidence).
VACTERL-like phenotypes v1.30 PLVAP Ivone Leong gene: PLVAP was added
gene: PLVAP was added to VACTERL-like phenotypes. Sources: Literature
Mode of inheritance for gene: PLVAP was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PLVAP were set to 29875123; 29661969; 26207260; 31215290
Phenotypes for gene: PLVAP were set to Diarrhoea 10, protein-losing enteropathy type, OMIM:618183
Review for gene: PLVAP was set to GREEN
Added comment: This gene is associated with a relevant phenotype in OMIM but not Gene2Phenotype. It is currently Amber with a recommendation to promote to Green on the Intestinal failure panel (Version 1.36) with the following reviews:

"Diarrhoea-10 is a protein-losing enteropathy characterized by intractable secretory diarrhoea and massive protein loss due to leaky fenestrated capillaries. Features include early-onset anasarca, severe hypoalbuminemia, hypogammaglobulinemia, and hypertriglyceridemia, as well as electrolyte abnormalities. Some patients exhibit facial dysmorphism and cardiac and renal anomalies. Intrafamilial variability has been observed, and the disease can be severe, with death occurring in infancy in some patients. Four unrelated families reported. Sources: Expert Review
Zornitza Stark (Australian Genomics), 5 Jan 2021"

"Comment on publications: PMID: 26207260. Patient is of Afgan descent born to consanguineous parents. Presented at 8 days of life with secretory diarrhea, metabolic acidosis, lethargy, poor feeding, and severe hyponatremia causing seizures. Further examination shows patient had bilateral colobomas, undescended testes, mildly dysplastic kidneys bilaterally, low-set ears, and micrognathia. PMID: 29875123. 2 patients (first cousins) from a Muslim Arab consanguineous kindred presented with anasarca, severe hypoalbuminaemia and hypogammaglobinaemia. PMID: 29661969. Patient is of Turkish descent born to consanguineous parents. Presented with severe haematochezia and moderate anasarca. Other findings: dysmorphism, metabolic acidosis, electrolyte deficiencies, elevated GGT, choroid plexus cysts, iris cysts, ASD, VSD, dilated megaureter with dilated renal pelvis, venous thrombosis. PMID: 31215290. Patient born to consanguineous parents. As well as intestinal phenotypes, she also had dysmorphic features, renal and cardiac phenotypes.
Ivone Leong (Genomics England Curator), 12 Apr 2021"

After discussion with the Geomics England Clinical Team it was decided that this gene should also be on this panel.
Sources: Literature
VACTERL-like phenotypes v1.29 WBP11 Eleanor Williams Classified gene: WBP11 as Green List (high evidence)
VACTERL-like phenotypes v1.29 WBP11 Eleanor Williams Added comment: Comment on list classification: Promoting from red to green as there are 5 cases from 3 families in which patients affected had features in three component organs
VACTERL-like phenotypes v1.29 WBP11 Eleanor Williams Gene: wbp11 has been classified as Green List (High Evidence).
VACTERL-like phenotypes v1.28 WBP11 Eleanor Williams gene: WBP11 was added
gene: WBP11 was added to VACTERL-like phenotypes. Sources: Literature
Mode of inheritance for gene: WBP11 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: WBP11 were set to 33276377
Phenotypes for gene: WBP11 were set to malformation syndrome affecting the cardiac, skeletal, gastrointestinal and renal systems
Review for gene: WBP11 was set to GREEN
Added comment: PMID: 33276377 - Martin et al 2020 - report 13 affected individuals from 7 unrelated families identified through various different cohort analysis (vertebral malformation, renal hypodysplasia, syndromic esophageal atresia, multiple congenital anomalies) in whom a WBP11 heterozygous variant is considered the top causative candidate. 5 identified variants were predicted to be protein truncating whilst the 6th was a missense variant. All variants are absent from population databases. In family 1, the variant was inherited from the apparently unaffected mother, indicating reduced penetrance, and phenotypic variance within families was observed. Phenotypes covered cardiac, vertebral, renal, craniofacial and gastrointestinal systems. At least at least 5 of the patients affected had features in three component organs so can be considered a VACTERL association. Wbp11 heterozygous null mice had vertebral and renal anomalies.
Sources: Literature
VACTERL-like phenotypes v1.27 KIAA1217 Eleanor Williams Classified gene: KIAA1217 as Amber List (moderate evidence)
VACTERL-like phenotypes v1.27 KIAA1217 Eleanor Williams Added comment: Comment on list classification: After consultation with the Genomics England clinical team rating this gene amber. Although there are 10 cases reported, the mode of inheritance and level of penterance is not clear, and it would be useful to have more information prior to diagnostic use
VACTERL-like phenotypes v1.27 KIAA1217 Eleanor Williams Gene: kiaa1217 has been classified as Amber List (Moderate Evidence).
VACTERL-like phenotypes v1.26 KIAA1217 Eleanor Williams gene: KIAA1217 was added
gene: KIAA1217 was added to VACTERL-like phenotypes. Sources: Literature
Mode of inheritance for gene: KIAA1217 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: KIAA1217 were set to 32369272
Phenotypes for gene: KIAA1217 were set to vertebral malformations
Review for gene: KIAA1217 was set to AMBER
Added comment: PMID: 32369272 - Al Dhaheri et al 2020 - 10 unrelated probands with vertebral malformations. 1 proband was compound heterozygous for variants in KIAA1217, the others were all heterozygous. 9 out of 11 variants are found in gnomad but a low allele frequency. In 3 patients (including the compound het) the variants were inherited from an unaffected parent, in the other 7 patients parental DNA was not available. Not associated with any phenotype in OMIM or Gene2Phenotype.
Sources: Literature
VACTERL-like phenotypes v1.25 Rebecca Foulger Panel types changed to Rare Disease 100K
VACTERL-like phenotypes v1.23 Ellen McDonagh List of related panels changed from to
Panel types changed to Rare Disease 100K; Component Of Super Panel
VACTERL-like phenotypes MIR17HG Louise Daugherty classified MIR17HG as Amber List (moderate evidence)
VACTERL-like phenotypes MIR17HG Louise Daugherty edited their review of MIR17HG
VACTERL-like phenotypes MIR17HG Louise Daugherty edited their review of MIR17HG
VACTERL-like phenotypes MIR17HG Louise Daugherty commented on MIR17HG
VACTERL-like phenotypes MIR17HG Louise Daugherty commented on MIR17HG
VACTERL-like phenotypes CHD4 Helen Brittain marked CHD4 as ready
VACTERL-like phenotypes CHD4 Helen Brittain classified CHD4 as Green List (high evidence)
VACTERL-like phenotypes CHD4 Helen Brittain Added gene to panel
VACTERL-like phenotypes PUF60 Louise Daugherty edited their review of PUF60
VACTERL-like phenotypes PUF60 Louise Daugherty commented on PUF60
VACTERL-like phenotypes KYNU Ellen McDonagh classified KYNU as green
VACTERL-like phenotypes HAAO Ellen McDonagh classified HAAO as green
VACTERL-like phenotypes HAAO Ellen McDonagh classified HAAO as amber
VACTERL-like phenotypes HAAO Ellen McDonagh added HAAO to panel
VACTERL-like phenotypes HAAO Ellen McDonagh reviewed HAAO
VACTERL-like phenotypes KYNU Ellen McDonagh commented on KYNU
VACTERL-like phenotypes KYNU Ellen McDonagh classified KYNU as amber
VACTERL-like phenotypes KYNU Ellen McDonagh added KYNU to panel
VACTERL-like phenotypes KYNU Ellen McDonagh reviewed KYNU
VACTERL-like phenotypes MIR17HG Ellen McDonagh commented on MIR17HG
VACTERL-like phenotypes PUF60 Richard Scott edited their review of PUF60
VACTERL-like phenotypes PUF60 Richard Scott classified PUF60 as green
VACTERL-like phenotypes PUF60 Richard Scott added PUF60 to panel
VACTERL-like phenotypes PUF60 Richard Scott reviewed PUF60
VACTERL-like phenotypes HOXA13 Richard Scott marked HOXA13 as ready
VACTERL-like phenotypes HOXA13 Richard Scott classified HOXA13 as green
VACTERL-like phenotypes HOXA13 Richard Scott added HOXA13 to panel
VACTERL-like phenotypes HOXA13 Richard Scott reviewed HOXA13