rs797045093
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_198525.3(KIF7):c.2944G>T(p.Glu982*) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000141 in 1,559,818 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 Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_198525.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF7 | ENST00000394412.8 | c.2944G>T | p.Glu982* | stop_gained | Exon 15 of 19 | 5 | NM_198525.3 | ENSP00000377934.3 | ||
KIF7 | ENST00000696512.1 | c.3067G>T | p.Glu1023* | stop_gained | Exon 15 of 19 | ENSP00000512678.1 | ||||
KIF7 | ENST00000677187.1 | n.618G>T | non_coding_transcript_exon_variant | Exon 3 of 7 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152240Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000591 AC: 1AN: 169128Hom.: 0 AF XY: 0.0000111 AC XY: 1AN XY: 90288
GnomAD4 exome AF: 0.0000149 AC: 21AN: 1407578Hom.: 0 Cov.: 38 AF XY: 0.0000144 AC XY: 10AN XY: 695206
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152240Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74368
ClinVar
Submissions by phenotype
Acrocallosal syndrome Pathogenic:2
The p.Glu982X variant in KIF7 has not been previously reported in individuals with disease and data from large population studies is insufficient to assess the frequency of this variant. This nonsense variant leads to a premature termination codon at position 982 which is predicted to lead to a truncated or absent protein. Loss of function variants in KIF7 have been shown to cause Acrocallosal syndrome. In summary, this variant meets our criteria to be classified as pathogenic for Acrocallosal syndrome in an autosomal recessive manner. -
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KIF7-related disorder Pathogenic:1
The KIF7 c.2944G>T variant is predicted to result in premature protein termination (p.Glu982*). This variant was reported in the compound heterozygous state in an individual with Joubert syndrome (Table S5, Bachmann-Gagescu et al. 2015. PubMed ID: 26092869). This variant is reported in 0.0024% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Nonsense variants in KIF7 are expected to be pathogenic. This variant is interpreted as pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at