rs387906984
Variant names:
Variant summary
Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_014918.5(CHSY1):c.205C>T(p.Gln69*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CHSY1
NM_014918.5 stop_gained
NM_014918.5 stop_gained
Scores
2
1
4
Clinical Significance
Conservation
PhyloP100: 0.394
Publications
2 publications found
Genes affected
CHSY1 (HGNC:17198): (chondroitin sulfate synthase 1) This gene encodes a member of the chondroitin N-acetylgalactosaminyltransferase family. These enzymes possess dual glucuronyltransferase and galactosaminyltransferase activity and play critical roles in the biosynthesis of chondroitin sulfate, a glycosaminoglycan involved in many biological processes including cell proliferation and morphogenesis. Decreased expression of this gene may play a role in colorectal cancer, and mutations in this gene are a cause of temtamy preaxial brachydactyly syndrome. [provided by RefSeq, Dec 2011]
CHSY1 Gene-Disease associations (from GenCC):
- temtamy preaxial brachydactyly syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 11 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 15-101251252-G-A is Pathogenic according to our data. Variant chr15-101251252-G-A is described in ClinVar as Pathogenic. ClinVar VariationId is 30712.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1255580Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 618074
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1255580
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
618074
African (AFR)
AF:
AC:
0
AN:
25798
American (AMR)
AF:
AC:
0
AN:
20774
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
20712
East Asian (EAS)
AF:
AC:
0
AN:
28368
South Asian (SAS)
AF:
AC:
0
AN:
59126
European-Finnish (FIN)
AF:
AC:
0
AN:
31878
Middle Eastern (MID)
AF:
AC:
0
AN:
5008
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1013006
Other (OTH)
AF:
AC:
0
AN:
50910
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Temtamy preaxial brachydactyly syndrome Pathogenic:1
Dec 10, 2010
OMIM
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:literature only
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
PhyloP100
Vest4
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
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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