rs387906561
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The ENST00000388918.10(TYRP1):c.107del(p.Leu36Ter) variant causes a frameshift 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). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
TYRP1
ENST00000388918.10 frameshift
ENST00000388918.10 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.10
Genes affected
TYRP1 (HGNC:12450): (tyrosinase related protein 1) This gene encodes a melanosomal enzyme that belongs to the tyrosinase family and plays an important role in the melanin biosynthetic pathway. Defects in this gene are the cause of rufous oculocutaneous albinism and oculocutaneous albinism type III. [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 9-12694100-CT-C is Pathogenic according to our data. Variant chr9-12694100-CT-C is described in ClinVar as [Pathogenic]. Clinvar id is 17597.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr9-12694100-CT-C is described in Lovd as [Pathogenic]. Variant chr9-12694100-CT-C is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TYRP1 | NM_000550.3 | c.107del | p.Leu36Ter | frameshift_variant | 2/8 | ENST00000388918.10 | NP_000541.1 | |
TYRP1 | XM_047423841.1 | c.107del | p.Leu36Ter | frameshift_variant | 2/5 | XP_047279797.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TYRP1 | ENST00000388918.10 | c.107del | p.Leu36Ter | frameshift_variant | 2/8 | 1 | NM_000550.3 | ENSP00000373570 | P1 | |
TYRP1 | ENST00000473763.1 | c.107del | p.Leu36Ter | frameshift_variant | 2/2 | 4 | ENSP00000419006 | |||
TYRP1 | ENST00000459790.1 | n.362del | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
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
Oculocutaneous albinism type 3 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 2006 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at