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Intellectual disability

Gene: CA2

Green List (high evidence)

CA2 (carbonic anhydrase 2)
EnsemblGeneIds (GRCh38): ENSG00000104267
EnsemblGeneIds (GRCh37): ENSG00000104267
OMIM: 611492, Gene2Phenotype
CA2 is in 8 panels

5 reviews

Louise Daugherty (Genomics England Curator)

Green List (high evidence)

Comment on phenotype. Reviewed literature and databases again due to Red review left by expert reviewer. However, there is still substantial evidence to support this gene being Green on the ID panel.
Carbonic anhydrase II deficiency syndrome is an autosomal recessive disorder that produces osteopetrosis, renal tubular acidosis, and cerebral calcification. Other features include mental retardation (seen in over 90 percent of reported cases), growth failure, and dental malocclusion. The carbonic anhydrase II gene is 20 kb, contains seven exons, and maps to chromosome 8q22. Sixteen distinct mutations have been identified in 110 reported patients. Nearly 65 percent of affected patients are homozygous for a splice junction mutation at the 5′ end of exon 2. Because of its prevalence among families of Arabic descent from Kuwait, Saudi Arabia, and North Africa, this mutation has been designated the “Arabic mutation” PMID:1301935. The second recurrent mutation, a frameshift in exon 7, is most prevalent in Caribbean Hispanic populations. The third recurrent mutation is His 107 toTyr, the first reported mutation. This mutation is due to a C to T transition in exon 3 and has been found in Belgian, Italian, Japanese and American patients (PMID: 1928091, 8834238, 1542674).
Created: 13 Aug 2018, 2:25 p.m.
From Gene2Phenotype: This is a confirmed biallelic gene for OSTEOPETROSIS AUTOSOMAL RECESSIVE TYPE 3. Patients in Decipher where the Pathogenicity is Pathogenic, all have intellectual disability/global developmental delay.
Created: 13 Aug 2018, 12:40 p.m.
Comment on publications: added publications suggested by external reviewers to support ID phenotype
Created: 13 Aug 2018, 12:15 p.m.

Zornitza Stark (Australian Genomics)

Red List (low evidence)

Definitely a green gene, but is this type of osteopetrosis associated with intellectual disability?
Created: 14 Jun 2018, 1:54 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Caroline Wright (Sanger)

Green List (high evidence)

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
OSTEOPETROSIS AUTOSOMAL RECESSIVE TYPE 3 (OPTB3)

Publications

BRIDGE consortium (NIHRBR-RD)

Green List (high evidence)

This is a pertinent gene from the NIHR BioResource - Rare Diseases Study (NIHRBR-RD) BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene is on the SPEED_NEURO_20170705 gene list. Evidences used for SPEED NEURO gene list: in_ddg2p_20141118_conf;in_ddg2p_20141118_conf;in_ddg2p_201507;in_ddg2p_201507_conf;in_ddg2p_2_4_2017;in_ddg2p_2_4_2017_conf;in_gilissen_2014_known . Main mutation mechanism : Loss of function
Created: 27 Jul 2017, 5:14 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : ddg2p_20141118; ddg2p_20141118_conf; ddg2p_201507; ddg2p_201507_conf; gilissen_2014_known; Nijmegen_ID_diagnostic; Nijmegen_ID_candidates; GEL_ID_green_20160217; neuro_20160418_strict; Loss of function. This is a pertinent gene from the BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene comes from the SPEED_NEURO_v3.0_20170404 gene list. The following experts from the BRIDGE consortium NIHRBR-RD contributed to this panel: - Professor F. Lucy Raymond, Cambridge Institute for Medical Research, University of Cambridge - Manju Kurian, Paediatric neurologist, Great Ormond Street Hosptial - Keren Carss, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Alba Sanchis-Juan, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Marie Erwood NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Louise Daugherty, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust
Created: 19 Jul 2017, 12:08 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Publications

Lu Raymond (university of cambridge )

Green List (high evidence)

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Osteopetrosis, autosomal recessive 3, with renal tubular acidosis, 259730
  • OSTEOPETROSIS AUTOSOMAL RECESSIVE TYPE 3 (OPTB3)
  • carbonic anhydrase II deficiency
  • intellectual disability
OMIM
611492
Clinvar variants
Variants in CA2
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

13 Aug 2018, Gel status: 3

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: CA2 were set to 25529582; 24896178; 12566520; 1301935; 8127074; 5041390; 16265785; 28509178; 15300855; 8834238; 1928091

13 Aug 2018, Gel status: 3

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: CA2 were set to 25529582; 24896178; 12566520; 1301935; 8127074; 5041390; 16265785; 28509178; 15300855

13 Aug 2018, Gel status: 3

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: CA2 were set to 25529582; 24896178; 12566520; 1301935; 8127074; 5041390; 16265785; 28509178

13 Aug 2018, Gel status: 3

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: CA2 were set to Osteopetrosis, autosomal recessive 3, with renal tubular acidosis, 259730; OSTEOPETROSIS AUTOSOMAL RECESSIVE TYPE 3 (OPTB3); carbonic anhydrase II deficiency; intellectual disability

13 Aug 2018, Gel status: 3

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: CA2 were set to 25529582; 24896178; 12566520; 1301935; 8127074; 5041390; 16265785

13 Aug 2018, Gel status: 3

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: CA2 were set to 25529582; 24896178; 12566520; 1301935; 8127074; 5041390

12 Mar 2018, Gel status: 3

Panel promoted to version 2.0

Ellen McDonagh (Genomics England Curator)

12.03.2018: Due to major updates completed (Phase 1, 2 and 3), this panel was promoted to Version 2 in order to reflect the major updates since November 2017 which have resulted in reviews for 836 genes added by Genomics England Curators and the Clinical Team, 130 new Green genes added to the interpretation pipeline (from 751 to 881 Green genes), and the gene total has increased from 1879 to 1927.

13 Nov 2015, Gel status: 4

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 4

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

CA2 was added to Intellectual disabilitypanel. Source: Expert Review Green

24 Jun 2015, Gel status: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

CA2 was added to Intellectual disabilitypanel. Sources: Radboud University Medical Center, Nijmegen