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Intellectual disability v5.313 KDM2B Eleanor Williams Tag gene-checked tag was added to gene: KDM2B.
Intellectual disability v5.313 KDM2B Eleanor Williams commented on gene: KDM2B
Intellectual disability v5.294 KDM2B Arina Puzriakova Tag Q2_23_promote_green was removed from gene: KDM2B.
Intellectual disability v5.286 KDM2B Arina Puzriakova reviewed gene: KDM2B: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v5.286 KDM2B Arina Puzriakova Source NHS GMS was added to KDM2B.
Source Expert Review Green was added to KDM2B.
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
Intellectual disability v5.165 KDM2B Achchuthan Shanmugasundram Deleted their comment
Intellectual disability v5.165 KDM2B Achchuthan Shanmugasundram Deleted their comment
Intellectual disability v5.165 KDM2B Achchuthan Shanmugasundram Deleted their comment
Intellectual disability v5.90 KDM2B Achchuthan Shanmugasundram Classified gene: KDM2B as Amber List (moderate evidence)
Intellectual disability v5.90 KDM2B Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be promoted to GREEN rating at the next GMS update.
Intellectual disability v5.90 KDM2B Achchuthan Shanmugasundram Gene: kdm2b has been classified as Amber List (Moderate Evidence).
Intellectual disability v5.89 KDM2B Achchuthan Shanmugasundram Classified gene: KDM2B as Amber List (moderate evidence)
Intellectual disability v5.89 KDM2B Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be promoted to GREEN rating at the next GMS update.
Intellectual disability v5.89 KDM2B Achchuthan Shanmugasundram Gene: kdm2b has been classified as Amber List (Moderate Evidence).
Intellectual disability v5.89 KDM2B Achchuthan Shanmugasundram Classified gene: KDM2B as Amber List (moderate evidence)
Intellectual disability v5.89 KDM2B Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be promoted to GREEN rating at the next GMS update.
Intellectual disability v5.89 KDM2B Achchuthan Shanmugasundram Gene: kdm2b has been classified as Amber List (Moderate Evidence).
Intellectual disability v5.89 KDM2B Achchuthan Shanmugasundram Classified gene: KDM2B as Amber List (moderate evidence)
Intellectual disability v5.89 KDM2B Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be promoted to GREEN rating at the next GMS update.
Intellectual disability v5.89 KDM2B Achchuthan Shanmugasundram Gene: kdm2b has been classified as Amber List (Moderate Evidence).
Intellectual disability v5.88 KDM2B Achchuthan Shanmugasundram Phenotypes for gene: KDM2B were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071
Intellectual disability v5.88 KDM2B Achchuthan Shanmugasundram Phenotypes for gene: KDM2B were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071
Intellectual disability v5.88 KDM2B Achchuthan Shanmugasundram Phenotypes for gene: KDM2B were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071
Intellectual disability v5.87 KDM2B Achchuthan Shanmugasundram Phenotypes for gene: KDM2B were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071
Intellectual disability v5.87 KDM2B Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: KDM2B.
Intellectual disability v5.87 KDM2B Achchuthan Shanmugasundram Phenotypes for gene: KDM2B were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071
Intellectual disability v5.88 KDM2B Achchuthan Shanmugasundram Phenotypes for gene: KDM2B were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071
Intellectual disability v5.88 KDM2B Achchuthan Shanmugasundram Phenotypes for gene: KDM2B were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071
Intellectual disability v5.87 KDM2B Achchuthan Shanmugasundram Phenotypes for gene: KDM2B were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071
Intellectual disability v5.88 KDM2B Achchuthan Shanmugasundram Phenotypes for gene: KDM2B were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071
Intellectual disability v5.87 KDM2B Achchuthan Shanmugasundram Phenotypes for gene: KDM2B were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071
Intellectual disability v5.88 KDM2B Achchuthan Shanmugasundram Phenotypes for gene: KDM2B were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071
Intellectual disability v5.88 KDM2B Achchuthan Shanmugasundram Phenotypes for gene: KDM2B were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071
Intellectual disability v5.88 KDM2B Achchuthan Shanmugasundram Phenotypes for gene: KDM2B were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071
Intellectual disability v5.87 KDM2B Achchuthan Shanmugasundram Phenotypes for gene: KDM2B were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071
Intellectual disability v5.88 KDM2B Achchuthan Shanmugasundram Phenotypes for gene: KDM2B were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071
Intellectual disability v5.88 KDM2B Achchuthan Shanmugasundram Phenotypes for gene: KDM2B were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071
Intellectual disability v5.87 KDM2B Achchuthan Shanmugasundram Phenotypes for gene: KDM2B were changed from to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071
Intellectual disability v5.87 KDM2B Achchuthan Shanmugasundram Publications for gene: KDM2B were set to 36322151
Intellectual disability v5.87 KDM2B Achchuthan Shanmugasundram Publications for gene: KDM2B were set to PMID: 36322151; 35128353; 35710456
Intellectual disability v5.86 KDM2B Achchuthan Shanmugasundram reviewed gene: KDM2B: Rating: GREEN; Mode of pathogenicity: None; Publications: 36322151; Phenotypes: neurodevelopmental disorder, MONDO:0700092, intellectual disability, MONDO:0001071; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v4.51 KDM2B Mike Spiller gene: KDM2B was added
gene: KDM2B was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: KDM2B was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: KDM2B were set to PMID: 36322151; 35128353; 35710456
Review for gene: KDM2B was set to GREEN
Added comment: van Jaarsveld et al 2022 PMID: 36322151

Majority of variants are missense, strong evidence for hotspot in CXXC domain.(7 different de Novo missenses + 1 de Novo in frame del. Same inframe del also found de novo in NHS GMS patient. All absent from gnomAD, region highly constrained).

Also 3 LOF SNVs and 3 patients with deletions including this gene, although not all are de novo and most also have potential alternate causes.

All have developmental delay. Almost all have intellectual disability ranging from mild to moderate, speech delay common..7 with cardiac abnormalities, 4 with kidney abnormalities.

Also 2 variants published in this region in PMID: 35710456, 35904121.

KDM2B methylation episignature recorded. CXXC variants show strong clustering, highly distinct from control dataset. LOF variants (including dels) also reported to show distinct episignature from controls, and from CXXC variants. While the data supports a KDM2B LOF episignature, this is not as clear, and may not be as specific, as the CXXC signature.

Mouse model also supports importance of CXXC domain, with mice heterozygous for CXXC-deleted KDM2B showing neurological defects (PMID: 35128353).

Evidence very strong for CXXC missenses less clear for haploinsufficiency.

Overall sufficient evidence from cases and episignature evidence to include as green for ID.
Sources: Literature