rs754279998
Variant summary
Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM1PM2PM4_SupportingPP5_Very_Strong
The NM_017777.4(MKS1):c.1115_1117delCCT(p.Ser372del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000217 in 1,613,288 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_017777.4 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151956Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249558Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135394
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461332Hom.: 0 AF XY: 0.0000234 AC XY: 17AN XY: 727020
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151956Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74218
ClinVar
Submissions by phenotype
Joubert syndrome 28 Pathogenic:2Other:1
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This variant is interpreted as Pathogenic for Joubert syndrome; Autosomal Recessive. PM1- Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation. PM2- Absent from controls or at extremely low frequency if recessive (0 homozygotes in gnomad). PM4- Protein length changes as a result of in-frame deletions/insertions in a non-repeat region or stop-loss variants. PP3- Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). PP5: Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation, 6 nonconflicting ClinVar entries, (PMIDs: 24886560, 26092869, 26490104 and 27570071). -
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Meckel syndrome, type 1 Pathogenic:2
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Bardet-Biedl syndrome 13 Pathogenic:2
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This variant was classified as: Pathogenic. This variant was detected in homozygous state. -
Bardet-Biedl syndrome 13;C3714506:Meckel syndrome, type 1;C4310705:Joubert syndrome 28 Pathogenic:2
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Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis Pathogenic:1
This variant, c.1115_1117del, results in the deletion of 1 amino acid(s) of the MKS1 protein (p.Ser372del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs754279998, gnomAD 0.003%). This variant has been observed in individual(s) with Joubert syndrome (PMID: 24886560, 26092869, 27570071). This variant is also known as c.1085_1088delCCT (p.S362del). ClinVar contains an entry for this variant (Variation ID: 217677). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. For these reasons, this variant has been classified as Pathogenic. -
Polydactyly;C0239399:Limb undergrowth;C0240595:Rotary nystagmus;C0557874:Global developmental delay;C1561643:Chronic kidney disease Pathogenic:1
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Familial aplasia of the vermis Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at