X-111401099-A-G

Variant names:

• chrX-111401099-A-G
• rs587783569
• NM_001195553.2:c.596T>C

Variant summary

Our verdict is Pathogenic. The variant received 17 ACMG points: 17P and 0B. PM1 PM2 PP2 PP3_Strong PP5_Very_Strong

The NM_001195553.2(DCX):​c.596T>C​(p.Leu199Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/20 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L199R) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 23)
• Consequence: DCX NM_001195553.2 missense
• Clinical Significance: Likely pathogenic criteria provided, multiple submitters, no conflicts P:2
• Conservation: PhyloP100: 9.32
• Publications: 0 publications found

Genes affected

DCX (HGNC:2714): (doublecortin) This gene encodes a member of the doublecortin family. The protein encoded by this gene is a cytoplasmic protein and contains two doublecortin domains, which bind microtubules. In the developing cortex, cortical neurons must migrate over long distances to reach the site of their final differentiation. The encoded protein appears to direct neuronal migration by regulating the organization and stability of microtubules. In addition, the encoded protein interacts with LIS1, the regulatory gamma subunit of platelet activating factor acetylhydrolase, and this interaction is important to proper microtubule function in the developing cortex. Mutations in this gene cause abnormal migration of neurons during development and disrupt the layering of the cortex, leading to epilepsy, cognitive disability, subcortical band heterotopia ("double cortex" syndrome) in females and lissencephaly ("smooth brain" syndrome) in males. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2010]

DCX Gene-Disease associations (from GenCC):

• lissencephaly spectrum disorders

  Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
• lissencephaly type 1 due to doublecortin gene mutation

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P
• subcortical band heterotopia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 17 ACMG points.

• PM1: In a hotspot region, there are 13 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 6 uncertain in NM_001195553.2
• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 87 curated pathogenic missense variants (we use a threshold of 10). The gene has 3 curated benign missense variants. Trascript score misZ: NaN (below the threshold of 3.09). GenCC associations: The gene is linked to lissencephaly type 1 due to doublecortin gene mutation, lissencephaly spectrum disorders, subcortical band heterotopia.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.941
• PP5: Variant X-111401099-A-G is Pathogenic according to our data. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111401099-A-G is described in CliVar as Likely_pathogenic. Clinvar id is 158487.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCX	NM_001195553.2	c.596T>C	p.Leu199Pro	missense_variant	Exon 3 of 7	ENST00000636035.2	NP_001182482.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCX	ENST00000636035.2	c.596T>C	p.Leu199Pro	missense_variant	Exon 3 of 7	2	NM_001195553.2	ENSP00000490614.1
DCX	ENST00000356220.8	c.596T>C	p.Leu199Pro	missense_variant	Exon 4 of 8	5		ENSP00000348553.4
DCX	ENST00000637453.1	c.596T>C	p.Leu199Pro	missense_variant	Exon 3 of 7	5		ENSP00000490357.1
DCX	ENST00000637570.1	c.596T>C	p.Leu199Pro	missense_variant	Exon 3 of 7	5		ENSP00000490878.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 23

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Ectopic tissue Pathogenic:1

Feb 08, 2013

Genetic Services Laboratory, University of Chicago

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Pathogenic:1

Aug 08, 2016

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The L199P variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The L199P variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species and in silico analysis predicts this variant is probably damaging to the protein structure/function. Furthermore, multiple missense variants in nearby residues have been reported in the Human Gene Mutation Database in association with DCX-related disorder (Stenson et al., 2014), supporting the functional importance of this region of the protein. Therefore, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.67	D
BayesDel_noAF	Pathogenic	0.73
CADD	Pathogenic	27
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.88	.;D;.;.;D;D;.;D;.
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Pathogenic	1.0	.;.;.;D;D;.;.;D;D
M_CAP	Pathogenic	0.81	D
MetaRNN	Pathogenic	0.94	D;D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.0059	D
PhyloP100		9.3
PrimateAI	Pathogenic	0.95	D
PROVEAN	Pathogenic	-5.8	.;.;.;D;.;D;D;.;.
REVEL	Pathogenic	0.97
Sift	Pathogenic	0.0	.;.;.;D;.;D;D;.;.
Sift4G	Uncertain	0.0030	.;.;.;D;.;D;D;.;.
Vest4		0.97, 0.99, 0.98
MVP		1.0
ClinPred		1.0	D
GERP RS		4.7
Varity_R		1.0
gMVP		1.0
Mutation Taster		=4/96	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs587783569; hg19: chrX-110644327;