NM_001099922.3:c.30C>T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4BP6_ModerateBP7
The NM_001099922.3(ALG13):c.30C>T(p.Thr10Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 24)
Exomes 𝑓: 9.1e-7 ( 0 hom. 1 hem. )
Failed GnomAD Quality Control
Consequence
ALG13
NM_001099922.3 synonymous
NM_001099922.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.886
Publications
0 publications found
Genes affected
ALG13 (HGNC:30881): (ALG13 UDP-N-acetylglucosaminyltransferase subunit) The protein encoded by this gene is a subunit of a bipartite UDP-N-acetylglucosamine transferase. It heterodimerizes with asparagine-linked glycosylation 14 homolog to form a functional UDP-GlcNAc glycosyltransferase that catalyzes the second sugar addition of the highly conserved oligosaccharide precursor in endoplasmic reticulum N-linked glycosylation. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2009]
ALG13 Gene-Disease associations (from GenCC):
- genetic developmental and epileptic encephalopathyInheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
- developmental and epileptic encephalopathy, 36Inheritance: XL Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P
- non-syndromic X-linked intellectual disabilityInheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.18).
BP6
Variant X-111681248-C-T is Benign according to our data. Variant chrX-111681248-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2737722.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.886 with no splicing effect.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
24
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 9.11e-7 AC: 1AN: 1098143Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 1AN XY: 363499 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1
AN:
1098143
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
363499
show subpopulations
African (AFR)
AF:
AC:
0
AN:
26398
American (AMR)
AF:
AC:
0
AN:
35199
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
19386
East Asian (EAS)
AF:
AC:
0
AN:
30204
South Asian (SAS)
AF:
AC:
1
AN:
54139
European-Finnish (FIN)
AF:
AC:
0
AN:
40526
Middle Eastern (MID)
AF:
AC:
0
AN:
4137
European-Non Finnish (NFE)
AF:
AC:
0
AN:
842061
Other (OTH)
AF:
AC:
0
AN:
46093
GnomAD4 genome
GnomAD4 genome
Cov.:
24
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Developmental and epileptic encephalopathy, 36 Benign:1
Jan 22, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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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