ClinVar Miner

Submissions for variant NM_198525.3(KIF7):c.3505C>T (p.Gln1169Ter)

gnomAD frequency: 0.00001  dbSNP: rs1963620354
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001355833 SCV001823950 pathogenic not provided 2021-11-03 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 28497568, 29146704)
Labcorp Genetics (formerly Invitae), Labcorp RCV005094474 SCV005838203 pathogenic Acrocallosal syndrome 2024-12-26 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gln1169*) in the KIF7 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in KIF7 are known to be pathogenic (PMID: 19666503, 21552264, 21633164, 26648833). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with Joubert syndrome (PMID: 28497568). ClinVar contains an entry for this variant (Variation ID: 1049562). For these reasons, this variant has been classified as Pathogenic.
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001355833 SCV001550833 pathogenic not provided no assertion criteria provided clinical testing The KIF7 p.Q1169* variant was identified in one homozygous individual with Joubert syndrome (Fleming_2017_PMID:29146704). The variant was not identified in dbSNP, ClinVar or in the following control databases: the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, or the Genome Aggregation Database (March 6, 2019, v2.1.1). The c.3505C>T variant leads to a premature stop codon at position 1169 which is predicted to lead to a truncated or absent protein and loss of function. Loss of function variants of the KIF7 gene are an established mechanism of disease in the autosomal recessive conditions: Acrocallosal syndrome, Joubert syndrome, Hydrolethalus syndrome, and Al-Gazali-Bakalinova syndrome.  In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic.

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