6-139373260-TAAG-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_006079.5(CITED2):c.682_684del(p.Leu228del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Consequence
CITED2
NM_006079.5 inframe_deletion
NM_006079.5 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.86
Genes affected
CITED2 (HGNC:1987): (Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 2) The protein encoded by this gene inhibits transactivation of HIF1A-induced genes by competing with binding of hypoxia-inducible factor 1-alpha to p300-CH1. Mutations in this gene are a cause of cardiac septal defects. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_006079.5. Strenght limited to Supporting due to length of the change: 1aa.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CITED2 | NM_006079.5 | c.682_684del | p.Leu228del | inframe_deletion | 2/2 | ENST00000367651.4 | NP_006070.2 | |
CITED2 | NM_001168388.3 | c.682_684del | p.Leu228del | inframe_deletion | 2/2 | NP_001161860.1 | ||
CITED2 | NM_001168389.3 | c.697_699del | p.Leu233del | inframe_deletion | 2/2 | NP_001161861.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CITED2 | ENST00000367651.4 | c.682_684del | p.Leu228del | inframe_deletion | 2/2 | 1 | NM_006079.5 | ENSP00000356623 | P1 | |
ENST00000650173.1 | n.510-55818_510-55816del | intron_variant, non_coding_transcript_variant | ||||||||
CITED2 | ENST00000536159.2 | c.682_684del | p.Leu228del | inframe_deletion | 2/2 | 3 | ENSP00000442831 | P1 | ||
CITED2 | ENST00000537332.2 | c.697_699del | p.Leu233del | inframe_deletion | 2/2 | 3 | ENSP00000444198 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Oct 17, 2019 | Not observed in large population cohorts (Lek et al., 2016); In-frame deletion of 1 amino acid in a non-repeat region; In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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
No publications associated with this variant yet.