NM_001145678.3:c.2173A>T
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_001145678.3(KIAA0825):c.2173A>T(p.Lys725*) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000457 in 1,531,282 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001145678.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIAA0825 | NM_001145678.3 | c.2173A>T | p.Lys725* | stop_gained | Exon 12 of 21 | ENST00000682413.1 | NP_001139150.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIAA0825 | ENST00000682413.1 | c.2173A>T | p.Lys725* | stop_gained | Exon 12 of 21 | NM_001145678.3 | ENSP00000506760.1 | |||
KIAA0825 | ENST00000504117.1 | n.1020A>T | non_coding_transcript_exon_variant | Exon 6 of 9 | 1 | |||||
KIAA0825 | ENST00000703867.1 | c.2173A>T | p.Lys725* | stop_gained | Exon 12 of 21 | ENSP00000515512.1 | ||||
KIAA0825 | ENST00000513200.7 | c.2173A>T | p.Lys725* | stop_gained | Exon 11 of 20 | 5 | ENSP00000424618.2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151942Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000652 AC: 1AN: 153322Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 81342
GnomAD4 exome AF: 0.00000362 AC: 5AN: 1379340Hom.: 0 Cov.: 26 AF XY: 0.00000147 AC XY: 1AN XY: 681252
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151942Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74218
ClinVar
Submissions by phenotype
Autosomal recessive nonsyndromic postaxial polydactyly Pathogenic:1
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Polydactyly, postaxial, type A1 Pathogenic:1
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Polydactyly, postaxial, type a10 Pathogenic:1
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not provided Uncertain:1
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene or region of a gene for which loss of function is not a well-established mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 30982135) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at