rs730882228
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM4PP5
The NM_017785.5(SPDL1):c.1724_1747del(p.Ser575_Thr582del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.00000479 in 1,460,780 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
SPDL1
NM_017785.5 inframe_deletion
NM_017785.5 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.40
Genes affected
SPDL1 (HGNC:26010): (spindle apparatus coiled-coil protein 1) This gene encodes a coiled-coil domain-containing protein that functions in mitotic spindle formation and chromosome segregation. The encoded protein plays a role in coordinating microtubule attachment by promoting recruitment of dynein proteins, and in mitotic checkpoint signaling. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_017785.5.
PP5
?
Variant 5-169604101-GAAAAGAAACTTCAAGCAAATTGGA-G is Pathogenic according to our data. Variant chr5-169604101-GAAAAGAAACTTCAAGCAAATTGGA-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 183325.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr5-169604101-GAAAAGAAACTTCAAGCAAATTGGA-G is described in Lovd as [Likely_pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPDL1 | NM_017785.5 | c.1724_1747del | p.Ser575_Thr582del | inframe_deletion | 12/12 | ENST00000265295.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPDL1 | ENST00000265295.9 | c.1724_1747del | p.Ser575_Thr582del | inframe_deletion | 12/12 | 1 | NM_017785.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1460780Hom.: 0 AF XY: 0.00000413 AC XY: 3AN XY: 726704
GnomAD4 exome
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7
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1460780
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3
AN XY:
726704
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Neonatal death;CN228308:Severe primary microcephaly Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | Dec 01, 2014 | - - |
Computational scores
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Name
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at