chr8-119067400-CCA-C
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_006438.5(COLEC10):c.128_129del(p.Thr43AsnfsTer9) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,752 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
COLEC10
NM_006438.5 frameshift
NM_006438.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.06
Genes affected
COLEC10 (HGNC:2220): (collectin subfamily member 10) This gene encodes a member of the C-lectin family, proteins that possess collagen-like sequences and carbohydrate recognition domains. The other members of this family are secreted proteins and bind to carbohydrate antigens on microorganisms facilitating their recognition and removal. This gene product is a cytosolic protein, a characteristic that suggests that it may have different biological functions than other C-lectins. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
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Very rare variant in population databases, with high coverage;
PP5
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Variant 8-119067400-CCA-C is Pathogenic according to our data. Variant chr8-119067400-CCA-C is described in ClinVar as [Pathogenic]. Clinvar id is 992663.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COLEC10 | NM_006438.5 | c.128_129del | p.Thr43AsnfsTer9 | frameshift_variant | 1/6 | ENST00000332843.3 | |
LOC101927513 | NR_134297.1 | n.1109+272_1109+273del | intron_variant, non_coding_transcript_variant | ||||
COLEC10 | NM_001324095.2 | c.-59-22271_-59-22270del | intron_variant | ||||
COLEC10 | XM_005250756.4 | c.-59-22271_-59-22270del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COLEC10 | ENST00000332843.3 | c.128_129del | p.Thr43AsnfsTer9 | frameshift_variant | 1/6 | 1 | NM_006438.5 | P1 | |
ENST00000518362.1 | n.1109+272_1109+273del | intron_variant, non_coding_transcript_variant | 1 | ||||||
COLEC10 | ENST00000521788.1 | n.236-22271_236-22270del | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152066Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250956Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135614
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GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461686Hom.: 0 AF XY: 0.00000413 AC XY: 3AN XY: 727136
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GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152066Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74292
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
3MC syndrome 3 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Medical Genetics Laboratory, Tarbiat Modares University | Jan 01, 2020 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at