rs150232843
Variant summary
Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PVS1PM2PP3PP5_Moderate
The NM_031433.4(MFRP):c.201G>A(p.Trp67Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,605,672 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_031433.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MFRP | NM_031433.4 | c.201G>A | p.Trp67Ter | stop_gained | 3/15 | ENST00000619721.6 | |
C1QTNF5 | NM_015645.5 | c.-2436G>A | 5_prime_UTR_variant | 3/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MFRP | ENST00000619721.6 | c.201G>A | p.Trp67Ter | stop_gained | 3/15 | 1 | NM_031433.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152104Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000130 AC: 3AN: 230000Hom.: 0 AF XY: 0.0000160 AC XY: 2AN XY: 124786
GnomAD4 exome AF: 0.0000124 AC: 18AN: 1453568Hom.: 0 Cov.: 36 AF XY: 0.00000692 AC XY: 5AN XY: 722134
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152104Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74302
ClinVar
Submissions by phenotype
Isolated microphthalmia 5 Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 26, 2010 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jan 08, 2020 | For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in MFRP are known to be pathogenic (PMID: 12140190, 15976030, 20361016). This variant has been observed to segregate with clinical features of MFRP-related conditions in a family (PMID: 20361016). ClinVar contains an entry for this variant (Variation ID: 183045). This variant is present in population databases (rs150232843, ExAC 0.003%). This sequence change creates a premature translational stop signal (p.Trp67*) in the MFRP gene. It is expected to result in an absent or disrupted protein product. - |
not provided Pathogenic:2
Pathogenic, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Pathogenic, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at