rs1557211410
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2PP5
The NM_006014.5(LAGE3):c.188+1G>A variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 25)
Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )
Failed GnomAD Quality Control
Consequence
LAGE3
NM_006014.5 splice_donor, intron
NM_006014.5 splice_donor, intron
Scores
2
3
Splicing: ADA: 0.9999
1
Clinical Significance
Conservation
PhyloP100: 1.72
Publications
3 publications found
Genes affected
LAGE3 (HGNC:26058): (L antigen family member 3) This gene belongs to the ESO/LAGE gene family, members of which are clustered together on chromosome Xq28, and have similar exon-intron structures. Unlike the other family members which are normally expressed only in testis and activated in a wide range of human tumors, this gene is ubiquitously expressed in somatic tissues. The latter, combined with the finding that it is highly conserved in mouse and rat, suggests that the encoded protein is functionally important. An intronless pseudogene with high sequence similarity to this gene is located on chromosome 9. [provided by RefSeq, Jul 2008]
LAGE3 Gene-Disease associations (from GenCC):
- Galloway-Mowat syndrome 2, X-linkedInheritance: XL Classification: STRONG, LIMITED Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
- Galloway-Mowat syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant X-154478727-C-T is Pathogenic according to our data. Variant chrX-154478727-C-T is described in ClinVar as Pathogenic. ClinVar VariationId is 444873.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 25
GnomAD3 genomes
Cov.:
25
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 969542Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 299014
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
969542
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
299014
African (AFR)
AF:
AC:
0
AN:
21202
American (AMR)
AF:
AC:
0
AN:
17375
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
13566
East Asian (EAS)
AF:
AC:
0
AN:
24832
South Asian (SAS)
AF:
AC:
0
AN:
38678
European-Finnish (FIN)
AF:
AC:
0
AN:
23832
Middle Eastern (MID)
AF:
AC:
0
AN:
3558
European-Non Finnish (NFE)
AF:
AC:
0
AN:
786163
Other (OTH)
AF:
AC:
0
AN:
40336
GnomAD4 genome Cov.: 25
GnomAD4 genome
Cov.:
25
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Galloway-Mowat syndrome 2, X-linked Pathogenic:1
Oct 25, 2017
OMIM
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:literature only
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
DANN
Uncertain
FATHMM_MKL
Benign
D
PhyloP100
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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