rs1555796939
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_000146.4(FTL):c.-189_-161del variant causes a 5 prime UTR 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 (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
FTL
NM_000146.4 5_prime_UTR
NM_000146.4 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.19
Genes affected
FTL (HGNC:3999): (ferritin light chain) This gene encodes the light subunit of the ferritin protein. Ferritin is the major intracellular iron storage protein in prokaryotes and eukaryotes. It is composed of 24 subunits of the heavy and light ferritin chains. Variation in ferritin subunit composition may affect the rates of iron uptake and release in different tissues. A major function of ferritin is the storage of iron in a soluble and nontoxic state. Defects in this light chain ferritin gene are associated with several neurodegenerative diseases and hyperferritinemia-cataract syndrome. This gene has multiple pseudogenes. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 19-48965317-GCGGTCCCGCGGGTCTGTCTCTTGCTTCAA-G is Pathogenic according to our data. Variant chr19-48965317-GCGGTCCCGCGGGTCTGTCTCTTGCTTCAA-G is described in ClinVar as [Pathogenic]. Clinvar id is 16478.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr19-48965317-GCGGTCCCGCGGGTCTGTCTCTTGCTTCAA-G is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FTL | NM_000146.4 | c.-189_-161del | 5_prime_UTR_variant | 1/4 | ENST00000331825.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FTL | ENST00000331825.11 | c.-189_-161del | 5_prime_UTR_variant | 1/4 | 1 | NM_000146.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Hereditary hyperferritinemia with congenital cataracts Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 19, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at