rs587779767
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_001371928.1(AHDC1):c.2898del(p.Tyr967ThrfsTer175) variant causes a frameshift 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 (★).
Frequency
Genomes: not found (cov: 33)
Consequence
AHDC1
NM_001371928.1 frameshift
NM_001371928.1 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.0110
Genes affected
AHDC1 (HGNC:25230): (AT-hook DNA binding motif containing 1) This gene encodes a protein containing two AT-hooks, which likely function in DNA binding. Mutations in this gene were found in individuals with Xia-Gibbs syndrome. [provided by RefSeq, Jun 2014]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. There are 31 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 1-27549217-AG-A is Pathogenic according to our data. Variant chr1-27549217-AG-A is described in ClinVar as [Pathogenic]. Clinvar id is 133327.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-27549217-AG-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AHDC1 | NM_001371928.1 | c.2898del | p.Tyr967ThrfsTer175 | frameshift_variant | 8/9 | ENST00000673934.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AHDC1 | ENST00000673934.1 | c.2898del | p.Tyr967ThrfsTer175 | frameshift_variant | 8/9 | NM_001371928.1 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:4
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | May 01, 2014 | - - |
Pathogenic, no assertion criteria provided | clinical testing | Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine | - | - - |
Hypotonia;C0037315:Sleep apnea;C0454644:Delayed speech and language development Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine | May 01, 2014 | - - |
Sleep apnea;C0454644:Delayed speech and language development;C0557874:Global developmental delay;C2267233:Neonatal hypotonia;C3714756:Intellectual disability Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Whole genome laboratory; Baylor College of Medicine | Apr 17, 2014 | - - |
Computational scores
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Calibrated prediction
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Prediction
Splicing
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Calibrated prediction
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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