rs122456134
Variant summary
Our verdict is Pathogenic. Variant got 15 ACMG points: 16P and 1B. PVS1PP5_Very_StrongBS2_Supporting
The ENST00000323022.10(CACNA1F):c.2872C>T(p.Arg958Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000557 in 1,077,004 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. 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
ENST00000323022.10 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1F | NM_001256789.3 | c.2872C>T | p.Arg958Ter | stop_gained | 24/48 | ENST00000323022.10 | NP_001243718.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1F | ENST00000323022.10 | c.2872C>T | p.Arg958Ter | stop_gained | 24/48 | 1 | NM_001256789.3 | ENSP00000321618 | ||
CACNA1F | ENST00000376265.2 | c.2905C>T | p.Arg969Ter | stop_gained | 24/48 | 1 | ENSP00000365441 | P1 | ||
CACNA1F | ENST00000376251.5 | c.2710C>T | p.Arg904Ter | stop_gained | 24/48 | 1 | ENSP00000365427 |
Frequencies
GnomAD3 genomes Cov.: 21
GnomAD4 exome AF: 0.00000557 AC: 6AN: 1077004Hom.: 0 Cov.: 33 AF XY: 0.00000571 AC XY: 2AN XY: 350434
GnomAD4 genome Cov.: 21
ClinVar
Submissions by phenotype
Congenital stationary night blindness 2A Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Clinical Genomics Laboratory, Washington University in St. Louis | Apr 12, 2024 | The CACNA1F c.2872C>T (p.Arg958*) variant has been observed in at least two individuals or families affected with X-linked congenital stationary night blindness, defined as either reduced visual acuity, nystagmus, strabismus, or a combination of these findings (Strom TM et al., PMID: 9662399; Zeitz C et al., PMID: 25307992). Furthermore, this variant has been reported in the ClinVar database as a germline pathogenic variant by several submitters. This variant causes a premature termination codon, which is predicted to lead to nonsense mediated decay. Additionally, other variants that introduce premature termination codons in this region have been described in affected individuals and are considered pathogenic (Wutz K et al., PMID: 12111638). Based on available information and the ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), this variant is classified as pathogenic. - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 01, 1998 | - - |
CACNA1F-related disorder Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | May 16, 2024 | The CACNA1F c.2905C>T variant is predicted to result in premature protein termination (p.Arg969*). This variant has been reported in a kindred with incomplete congenital stationary night blindness (reported as 2172C>T, R958X in Strom et al. 1998. PubMed ID: 9662399) and in an individual with reduced visual acuity and nystagmus (Thomas et al. 2017. PubMed ID: 28378818). This variant has not been reported in a large population database, indicating this variant is rare. Nonsense variants in CACNA1F are expected to be pathogenic. This variant is interpreted as pathogenic. - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 15, 2022 | For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. ClinVar contains an entry for this variant (Variation ID: 11615). This variant is also known as p.Arg958*. This premature translational stop signal has been observed in individual(s) with incomplete congenital stationary night blindness (PMID: 9662399). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg969*) in the CACNA1F gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CACNA1F are known to be pathogenic (PMID: 9662399, 11281458, 17525176, 22194652, 24124559, 26992781). - |
Retinal dystrophy Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Blueprint Genetics | Oct 30, 2018 | - - |
Congenital stationary night blindness Pathogenic:1
Pathogenic, no assertion criteria provided | research | NIHR Bioresource Rare Diseases, University of Cambridge | Jan 01, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at