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

Genomes: not found (cov: 21)
Exomes 𝑓: 0.0000056 ( 0 hom. 2 hem. )

Consequence

CACNA1F
ENST00000323022.10 stop_gained

Scores

2
2
1

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:6

Conservation

PhyloP100: 2.13
Variant links:
Genes affected
CACNA1F (HGNC:1393): (calcium voltage-gated channel subunit alpha1 F) This gene encodes a multipass transmembrane protein that functions as an alpha-1 subunit of the voltage-dependent calcium channel, which mediates the influx of calcium ions into the cell. The encoded protein forms a complex of alpha-1, alpha-2/delta, beta, and gamma subunits in a 1:1:1:1 ratio. Mutations in this gene can cause X-linked eye disorders, including congenital stationary night blindness type 2A, cone-rod dystropy, and Aland Island eye disease. Alternatively spliced transcript variants encoding multiple isoforms have been observed. [provided by RefSeq, Aug 2013]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 15 ACMG points.

PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PP5
Variant X-49218511-G-A is Pathogenic according to our data. Variant chrX-49218511-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 11615.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-49218511-G-A is described in Lovd as [Pathogenic]. Variant chrX-49218511-G-A is described in Lovd as [Pathogenic].
BS2
High Hemizygotes in GnomAdExome4 at 2 XL geneVariant has number of hemizygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CACNA1FNM_001256789.3 linkuse as main transcriptc.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
CACNA1FENST00000323022.10 linkuse as main transcriptc.2872C>T p.Arg958Ter stop_gained 24/481 NM_001256789.3 ENSP00000321618 O60840-2
CACNA1FENST00000376265.2 linkuse as main transcriptc.2905C>T p.Arg969Ter stop_gained 24/481 ENSP00000365441 P1O60840-1
CACNA1FENST00000376251.5 linkuse as main transcriptc.2710C>T p.Arg904Ter stop_gained 24/481 ENSP00000365427 O60840-4

Frequencies

GnomAD3 genomes
Cov.:
21
GnomAD4 exome
AF:
0.00000557
AC:
6
AN:
1077004
Hom.:
0
Cov.:
33
AF XY:
0.00000571
AC XY:
2
AN XY:
350434
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000721
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
21
Bravo
AF:
0.00000378

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Congenital stationary night blindness 2A Pathogenic:2
Pathogenic, criteria provided, single submitterclinical testingClinical Genomics Laboratory, Washington University in St. LouisApr 12, 2024The 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 providedliterature onlyOMIMJul 01, 1998- -
CACNA1F-related disorder Pathogenic:1
Pathogenic, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesMay 16, 2024The 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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpAug 15, 2022For 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 submitterclinical testingBlueprint GeneticsOct 30, 2018- -
Congenital stationary night blindness Pathogenic:1
Pathogenic, no assertion criteria providedresearchNIHR Bioresource Rare Diseases, University of CambridgeJan 01, 2015- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.74
D
BayesDel_noAF
Pathogenic
0.60
CADD
Pathogenic
38
DANN
Uncertain
1.0
FATHMM_MKL
Uncertain
0.91
D
MutationTaster
Benign
1.0
A;A;A
Vest4
0.84
GERP RS
4.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.26
Details are displayed if max score is > 0.2
DS_DG_spliceai
0.26
Position offset: 2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs122456134; hg19: chrX-49074970; COSMIC: COSV100544544; COSMIC: COSV100544544; API