11-681044-CCTT-C
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Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM4_SupportingPP5_Moderate
The NM_021008.4(DEAF1):c.913_915del(p.Lys305del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.00000657 in 152,098 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Consequence
DEAF1
NM_021008.4 inframe_deletion
NM_021008.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.90
Genes affected
DEAF1 (HGNC:14677): (DEAF1 transcription factor) This gene encodes a zinc finger domain-containing protein that functions as a regulator of transcription. The encoded proteins binds to its own promoter as well as to that of several target genes. Activity of this protein is important in the regulation of embryonic development. Mutations in this gene have been found in individuals with autosomal dominant cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_021008.4. Strenght limited to Supporting due to length of the change: 1aa.
PP5
Variant 11-681044-CCTT-C is Pathogenic according to our data. Variant chr11-681044-CCTT-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 437397.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DEAF1 | NM_021008.4 | c.913_915del | p.Lys305del | inframe_deletion | 7/12 | ENST00000382409.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DEAF1 | ENST00000382409.4 | c.913_915del | p.Lys305del | inframe_deletion | 7/12 | 1 | NM_021008.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152098Hom.: 0 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152098Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74298
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ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Intellectual disability, autosomal dominant 24 Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 2020 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Aug 17, 2017 | This variant has been observed once in our laboratory de novo in a 3-year-old female with central hypotonia, global delays, ataxia, seizure disorder, autism spectrum disorder. A de novo DYNC1H1 missense variant was also present. - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at