rs200691042
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_001201543.2(FAM161A):c.1309A>T(p.Arg437Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000416 in 1,614,194 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. R437R) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001201543.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM161A | NM_001201543.2 | c.1309A>T | p.Arg437Ter | stop_gained | 3/7 | ENST00000404929.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM161A | ENST00000404929.6 | c.1309A>T | p.Arg437Ter | stop_gained | 3/7 | 1 | NM_001201543.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000276 AC: 42AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000281 AC: 70AN: 249396Hom.: 0 AF XY: 0.000229 AC XY: 31AN XY: 135306
GnomAD4 exome AF: 0.000430 AC: 629AN: 1461892Hom.: 1 Cov.: 31 AF XY: 0.000386 AC XY: 281AN XY: 727246
GnomAD4 genome ? AF: 0.000276 AC: 42AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74484
ClinVar
Submissions by phenotype
Retinitis pigmentosa 28 Pathogenic:8
Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Dec 30, 2020 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Genetics and Molecular Pathology, SA Pathology | Jan 21, 2022 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 10, 2010 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Oct 18, 2016 | - - |
Pathogenic, criteria provided, single submitter | research | Ocular Genomics Institute, Massachusetts Eye and Ear | Apr 08, 2021 | The FAM161A c.1309A>T variant was identified in an individual with retinitis pigmentosa with a presumed recessive inheritance pattern. Through a review of available evidence we were able to apply the following criteria: PVS1, PM2, PM3. Based on this evidence we have classified this variant as Pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Genomics England Pilot Project, Genomics England | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 25, 2024 | - - |
not provided Pathogenic:8
Pathogenic, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2023 | FAM161A: PM3:Very Strong, PVS1, PM2 - |
Pathogenic, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 15, 2016 | - - |
Pathogenic, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | This sequence change creates a premature translational stop signal (p.Arg437*) in the FAM161A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FAM161A are known to be pathogenic (PMID: 20705278, 20705279, 24651477). This variant is present in population databases (rs200691042, gnomAD 0.05%). This premature translational stop signal has been observed in individuals with FAM161A-related conditions (PMID: 20705278, 26113502, 26574802). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 36). For these reasons, this variant has been classified as Pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Feb 09, 2022 | Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 30718709, 25097241, 25525159, 20705278, 28559085, 26113502, 26574802, 25999674, 31589614, 34426522, 33576794) - |
Pathogenic, criteria provided, single submitter | clinical testing | Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen | Sep 15, 2021 | - - |
Retinitis pigmentosa Pathogenic:4
Pathogenic, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Pathogenic, no assertion criteria provided | research | Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet | Apr 01, 2018 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Sep 19, 2017 | The FAM161A c.1309A>T (p.Arg437Ter) variant has been reported in at least five studies in 18 individuals with autosomal recessive retinitis pigmentosa, including 12 in a homozygous state, five in a compound heterozygous state, and one in a heterozygous state in whom a second variant was not identified (Langmann et al. 2010; Wang et al. 2014; Rose et al. 2015; Van Schil et al. 2015; van Huet et al. 2015). These patients were unrelated, except for two sets of siblings who were homozygous for the p.Arg437Ter variant (Van Schil et al. 2015; Rose et al. 2015). The p.Arg437Ter variant was absent from 400 control chromosomes and is reported at a frequency of 0.00061 in the European American population of the Exome Sequencing Project. Based on the collective evidence, the p.Arg437Ter variant is classified as pathogenic for autosomal recessive retinitis pigmentosa. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. - |
Pathogenic, criteria provided, single submitter | curation | Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard | Apr 01, 2021 | The p.Arg437Ter variant in FAM161A was identified in an individual with Retinitis pigmentosa, via a collaborative study between the Broad Institute's Center for Mendelian Genomics and the Pierce lab (https://oculargenomics.meei.harvard.edu/labs/pierce-lab/lab-members/). Through a review of available evidence we were able to apply the following criteria: PVS1, PM2, PM3. Based on this evidence we have classified this variant as Pathogenic. If you have any questions about the classification please reach out to the Pierce Lab. - |
Retinal dystrophy Pathogenic:2
Pathogenic, no assertion criteria provided | research | Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet | Apr 01, 2018 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Blueprint Genetics | Jun 16, 2019 | - - |
Cone-rod dystrophy Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | Sep 01, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at