rs771852530
Variant names:
Your query was ambiguous. Multiple possible variants found:
- chrX-100661933-GTTTTTTTTTTTTTTT-G
- chrX-100661933-GTTTTTTTTTTTTTTT-GT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTTTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTTTTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTTTTTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTTTTTTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTTTTTTTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTTTTTTTTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTTTTTTTTTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTTTTTTTTTTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTTTTTTTTTTTTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTTTTTTTTTTTTTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTTTTTTTTTTTTTTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTTTTTTTTTTTTTTTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTTTTTTTTTTTTTTTTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTTTTTTTTTTTTTTTTTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTTTTTTTTTTTTTTTTTTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTTTTTTTTTTTTTTTTTTTTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTTTTTTTTTTTTTTTTTTTTTTT
- chrX-100661933-GTTTTTTTTTTTTTTT-GTTTTTTTTTTTTTTTTTTTTTTTTTT
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_014467.3(SRPX2):c.164-231_164-217delTTTTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000017 ( 0 hom., 0 hem., cov: 16)
Consequence
SRPX2
NM_014467.3 intron
NM_014467.3 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.07
Publications
0 publications found
Genes affected
SRPX2 (HGNC:30668): (sushi repeat containing protein X-linked 2) This gene encodes a secreted protein that contains three sushi repeat motifs. The encoded protein may play a role in the development of speech and language centers in the brain. This protein may also be involved in angiogenesis. Mutations in this gene are the cause of bilateral perisylvian polymicrogyria, rolandic epilepsy, speech dyspraxia and cognitive disability. [provided by RefSeq, May 2010]
SRPX2 Gene-Disease associations (from GenCC):
- rolandic epilepsy-speech dyspraxia syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- polymicrogyria, bilateral perisylvian, X-linkedInheritance: XL Classification: LIMITED Submitted by: G2P
- rolandic epilepsy, intellectual disability, and speech dyspraxia, X-linkedInheritance: XL Classification: LIMITED, NO_KNOWN Submitted by: PanelApp Australia, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- epilepsyInheritance: XL Classification: NO_KNOWN Submitted by: ClinGen
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_014467.3. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SRPX2 | TSL:1 MANE Select | c.164-242_164-228delTTTTTTTTTTTTTTT | intron | N/A | ENSP00000362095.3 | O60687 | |||
| SRPX2 | TSL:5 | c.164-218_164-204delTTTTTTTTTTTTTTT | intron | N/A | ENSP00000492168.1 | A0A1W2PR88 | |||
| SRPX2 | TSL:5 | c.164-242_164-228delTTTTTTTTTTTTTTT | intron | N/A | ENSP00000492571.1 | A0A1W2PRB1 |
Frequencies
GnomAD3 genomes 0.0000168 AC: 1AN: 59698Hom.: 0 Cov.: 16 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
59698
Hom.:
Cov.:
16
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.0000168 AC: 1AN: 59698Hom.: 0 Cov.: 16 AF XY: 0.00 AC XY: 0AN XY: 13234 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
59698
Hom.:
Cov.:
16
AF XY:
AC XY:
0
AN XY:
13234
show subpopulations
African (AFR)
AF:
AC:
0
AN:
14088
American (AMR)
AF:
AC:
0
AN:
5357
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
1672
East Asian (EAS)
AF:
AC:
0
AN:
1875
South Asian (SAS)
AF:
AC:
0
AN:
1163
European-Finnish (FIN)
AF:
AC:
0
AN:
1650
Middle Eastern (MID)
AF:
AC:
0
AN:
115
European-Non Finnish (NFE)
AF:
AC:
1
AN:
32521
Other (OTH)
AF:
AC:
0
AN:
807
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.875
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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