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Intellectual disability

Gene: KIF2A

Green List (high evidence)

KIF2A (kinesin family member 2A)
EnsemblGeneIds (GRCh38): ENSG00000068796
EnsemblGeneIds (GRCh37): ENSG00000068796
OMIM: 602591, Gene2Phenotype
KIF2A is in 5 panels

6 reviews

Catherine Snow (Genomics England)

Three further cases identified in the literature.
PMID:27747449 (Cavallin et al 2017) detected two de novo p.Ser317Asn and p.His321Pro mutations in KIF2A in two patients with lissencephaly and microcephaly. Case 1 had DD, no epilepsy but was only 9 months old at last reporting. Case 2 had neonatal seizures and severe DD.
PMID:27896282 (Tian et al 2016) report a patient with lissencephaly, developmental delay, and infantile spasms, due to de novo heterozygous variant in KIF2A (p.Thr320Ile).
Most cases identified have epilepsy first however as one individual did not have seizures KIF2A is relevant for the ID panel.
Therefore upgrading rating from Amber to Green as now sufficient (>3) unrelated cases.
Created: 24 Jul 2019, 10:38 a.m. | Last Modified: 25 Jul 2019, 8:29 a.m.
Panel Version: 2.977

Konstantinos Varvagiannis (Other)

Green List (high evidence)

Further to the articles that have been cited previously, 3 additional individuals with KIF2A de novo variants and a similar phenotype have been reported:

PMID 27747449 reports on a 9 month-old female with congenital microcephaly and posteriorly predominant lissencephaly, with a de novo missense variant (p.Ser317Asn) in KIF2A. A second patient with lissencephaly of the same type and severe ID is described. This individual was found to have a de novo missense variant in KIF2A (p.His321Pro). The authors have excluded alternative causes (gene panel analysis and prior aCGH performed for both patients). p.Ser317 and p.His321 are proposed as hotspots since the first variant (Ser317Asn) was previously described, while His321Pro concerns the same AA as in a previously described individual (His321Asp) [both in PMID 23603762].

PMID 27896282 reports on a 9 month-old female with lissencephaly and a de novo missense variant p.Thr320Ile. Expression studies were suggestive of a different pattern of cellular localization compared to wt and of abnormal microtubules.

This variant has also been submitted as likely pathogenic in ClinVar by a (seemingly) different submitter (Variation 435642).

[The variants in the different articles would correspond to the same AA positions whether NM_004520 or NM_001098511 is used as a reference sequence].
Created: 13 Aug 2018, 12:23 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Phenotypes
MALFORMATIONS OF CORTICAL DEVELOPMENT AND MICROCEPHALY

Publications

Olivia Niblock (Genomics England Curator)

I don't know

Amber - two reports of different variants in this gene linked to severe developmental delay, amongst other phenotypes (PMID:23603762). There is a 5q12 deletion reported in the literature which encompasses this gene and eleven others - patients have been noted to express mental retardation(PMID:21594994)
Created: 13 Dec 2017, 10:16 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Publications

Caroline Wright (Sanger)

I don't know

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
MALFORMATIONS OF CORTICAL DEVELOPMENT AND MICROCEPHALY.

Publications

Lu Raymond (university of cambridge )

I don't know

Richard Scott (Genomics England Curator)

Comment on list classification: 2 cases reported to date. Pending further data before diagnostic
Created: 7 Feb 2016, 9:35 p.m.

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Green
Phenotypes
  • Cortical dysplasia, complex, with other brain malformations 3, 615411
OMIM
602591
Clinvar variants
Variants in KIF2A
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

24 Jul 2019, Gel status: 3

Entity classified by Genomics England curator

Catherine Snow (Genomics England)

Gene: kif2a has been classified as Green List (High Evidence).

24 Jul 2019, Gel status: 2

Set Phenotypes

Catherine Snow (Genomics England)

Phenotypes for gene: KIF2A were changed from Cortical dysplasia, complex, with other brain malformations 3, 615411 to Cortical dysplasia, complex, with other brain malformations 3, 615411

24 Jul 2019, Gel status: 2

Set Phenotypes

Catherine Snow (Genomics England)

Phenotypes for gene: KIF2A were changed from Cortical dysplasia, complex, with other brain malformations 3, 615411 to Cortical dysplasia, complex, with other brain malformations 3, 615411

24 Jul 2019, Gel status: 2

Set Phenotypes

Catherine Snow (Genomics England)

Phenotypes for gene: KIF2A were changed from MALFORMATIONS OF CORTICAL DEVELOPMENT AND MICROCEPHALY. to Cortical dysplasia, complex, with other brain malformations 3, 615411

23 Jul 2019, Gel status: 2

Set publications

Catherine Snow (Genomics England)

Publications for gene: KIF2A were set to 23603762; 21594994; 27747449; 27896282

23 Jul 2019, Gel status: 2

Set publications

Catherine Snow (Genomics England)

Publications for gene: KIF2A were set to 23603762; 21594994; 27747449; 27896282

23 Jul 2019, Gel status: 2

Set publications

Catherine Snow (Genomics England)

Publications for gene: KIF2A were set to 23603762; 21594994

12 Mar 2018, Gel status: 2

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.

5 Jan 2018, Gel status: 2

Added New Source, Set mode of inheritance, Set publications

Ellen McDonagh (Genomics England Curator)

Expert Review Amber was added to KIF2A. Panel: Intellectual disability Model of inheritance for gene KIF2A was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene KIF2A was set to ['23603762', ' 21594994']

7 Feb 2016, Gel status: 1

Gene classified by Genomics England curator

Richard Scott (Genomics England Curator)

This gene has been classified as Red List (Low Evidence).

7 Feb 2016, Gel status: 1

Gene classified by Genomics England curator

Richard Scott (Genomics England Curator)

This gene has been classified as Red List (Low Evidence).

13 Nov 2015, Gel status: 2

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 2

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 0

Created

Ellen McDonagh (Genomics England Curator)

KIF2A was created by ellenmcdonagh

13 Nov 2015, Gel status: 0

Added New Source

Ellen McDonagh (Genomics England Curator)

KIF2A was added to Intellectual disabilitypanel. Sources: Expert Review Amber