rs587783531
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001195553.2(DCX):c.195C>T(p.Phe65Phe) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000897 in 111,519 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000090 ( 0 hom., 1 hem., cov: 22)
Consequence
DCX
NM_001195553.2 synonymous
NM_001195553.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.57
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DCX | NM_001195553.2 | c.195C>T | p.Phe65Phe | synonymous_variant | 2/7 | ENST00000636035.2 | NP_001182482.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DCX | ENST00000636035.2 | c.195C>T | p.Phe65Phe | synonymous_variant | 2/7 | 2 | NM_001195553.2 | ENSP00000490614.1 | ||
DCX | ENST00000356220.8 | c.195C>T | p.Phe65Phe | synonymous_variant | 3/8 | 5 | ENSP00000348553.4 | |||
DCX | ENST00000637453.1 | c.195C>T | p.Phe65Phe | synonymous_variant | 2/7 | 5 | ENSP00000490357.1 | |||
DCX | ENST00000637570.1 | c.195C>T | p.Phe65Phe | synonymous_variant | 2/7 | 5 | ENSP00000490878.1 |
Frequencies
GnomAD3 genomes AF: 0.00000897 AC: 1AN: 111519Hom.: 0 Cov.: 22 AF XY: 0.0000297 AC XY: 1AN XY: 33705
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GnomAD4 exome Cov.: 32
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GnomAD4 genome AF: 0.00000897 AC: 1AN: 111519Hom.: 0 Cov.: 22 AF XY: 0.0000297 AC XY: 1AN XY: 33705
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: -42
DS_DG_spliceai
Position offset: 33
Find out detailed SpliceAI scores and Pangolin per-transcript scores at