rs1555600644

Variant names:

• chr17-58216279-CATTATAATACATCAAACTTTTGCTTCTGTAACTGTTTAATCAAATCAGTTCTACAGAACTGATGCTATCTGACATGTTTTCATAACCAACACTAAACTAATGAATGGCAGGGGAACCAAGAACATTAGAGCTAAAAGGAACCA-C
• rs1555600644
• NM_017777.4:c.262-179_262-37del

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP5_Moderate

The NM_017777.4(MKS1):​c.262-179_262-37del variant causes a intron 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 (★). There are indicators that this mutation may affect the branch point..

• Frequency: Genomes: not found (cov: 32)
• Consequence: MKS1 NM_017777.4 intron
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 3.05

Genes affected

MKS1 (HGNC:7121): (MKS transition zone complex subunit 1) The protein encoded by this gene localizes to the basal body and is required for formation of the primary cilium in ciliated epithelial cells. Mutations in this gene result in Meckel syndrome type 1 and in Bardet-Biedl syndrome type 13. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 17-58216279-CATTATAATACATCAAACTTTTGCTTCTGTAACTGTTTAATCAAATCAGTTCTACAGAACTGATGCTATCTGACATGTTTTCATAACCAACACTAAACTAATGAATGGCAGGGGAACCAAGAACATTAGAGCTAAAAGGAACCA-C is Pathogenic according to our data. Variant chr17-58216279-CATTATAATACATCAAACTTTTGCTTCTGTAACTGTTTAATCAAATCAGTTCTACAGAACTGATGCTATCTGACATGTTTTCATAACCAACACTAAACTAATGAATGGCAGGGGAACCAAGAACATTAGAGCTAAAAGGAACCA-C is described in ClinVar as [Pathogenic]. Clinvar id is 217674.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-58216279-CATTATAATACATCAAACTTTTGCTTCTGTAACTGTTTAATCAAATCAGTTCTACAGAACTGATGCTATCTGACATGTTTTCATAACCAACACTAAACTAATGAATGGCAGGGGAACCAAGAACATTAGAGCTAAAAGGAACCA-C is described in Lovd as [Likely_pathogenic]. Variant chr17-58216279-CATTATAATACATCAAACTTTTGCTTCTGTAACTGTTTAATCAAATCAGTTCTACAGAACTGATGCTATCTGACATGTTTTCATAACCAACACTAAACTAATGAATGGCAGGGGAACCAAGAACATTAGAGCTAAAAGGAACCA-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MKS1	NM_017777.4	c.262-179_262-37del		intron_variant	Intron 3 of 17	ENST00000393119.7	NP_060247.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MKS1	ENST00000393119.7	c.262-179_262-37del		intron_variant	Intron 3 of 17	1	NM_017777.4	ENSP00000376827.2

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Familial aplasia of the vermis Pathogenic:1

Feb 23, 2015

UW Hindbrain Malformation Research Program, University of Washington

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BranchPoint Hunter		3.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1555600644; hg19: chr17-56293640;