rs869312721
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM4_SupportingPP5_Moderate
The NM_017671.5(FERMT1):c.1867_1869del(p.Ile623del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,856 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
FERMT1
NM_017671.5 inframe_deletion
NM_017671.5 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.20
Genes affected
FERMT1 (HGNC:15889): (FERM domain containing kindlin 1) This gene encodes a member of the fermitin family, and contains a FERM domain and a pleckstrin homology domain. The encoded protein is involved in integrin signaling and linkage of the actin cytoskeleton to the extracellular matrix. Mutations in this gene have been linked to Kindler syndrome. [provided by RefSeq, Dec 2009]
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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_017671.5. Strenght limited to Supporting due to length of the change: 1aa.
PP5
?
Variant 20-6077337-CGAT-C is Pathogenic according to our data. Variant chr20-6077337-CGAT-C is described in ClinVar as [Pathogenic]. Clinvar id is 224168.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr20-6077337-CGAT-C is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FERMT1 | NM_017671.5 | c.1867_1869del | p.Ile623del | inframe_deletion | 15/15 | ENST00000217289.9 | |
FERMT1 | XM_024451935.2 | c.1867_1869del | p.Ile623del | inframe_deletion | 15/15 | ||
FERMT1 | XM_047440259.1 | c.1867_1869del | p.Ile623del | inframe_deletion | 15/15 | ||
FERMT1 | XM_047440260.1 | c.1582_1584del | p.Ile528del | inframe_deletion | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FERMT1 | ENST00000217289.9 | c.1867_1869del | p.Ile623del | inframe_deletion | 15/15 | 1 | NM_017671.5 | P1 | |
FERMT1 | ENST00000478194.1 | n.827_829del | non_coding_transcript_exon_variant | 7/7 | 1 | ||||
FERMT1 | ENST00000536936.1 | c.*1369_*1371del | 3_prime_UTR_variant, NMD_transcript_variant | 14/14 | 1 | ||||
FERMT1 | ENST00000699095.1 | c.1867_1869del | p.Ile623del | inframe_deletion | 14/14 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461856Hom.: 0 AF XY: 0.00000275 AC XY: 2AN XY: 727230
GnomAD4 exome
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1461856
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727230
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
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Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Kindler syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | research | Biomedical Innovation Departament, CIEMAT | Feb 08, 2010 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at