chr1-77916129-CTGAGG-C
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Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 10P and 4B. PVS1PM2BS2
The NM_144573.4(NEXN):c.25_27+2del variant causes a splice donor, coding sequence change. The variant allele was found at a frequency of 0.00000344 in 1,452,972 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
NEXN
NM_144573.4 splice_donor, coding_sequence
NM_144573.4 splice_donor, coding_sequence
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.37
Genes affected
NEXN (HGNC:29557): (nexilin F-actin binding protein) This gene encodes a filamentous actin-binding protein that may function in cell adhesion and migration. Mutations in this gene have been associated with dilated cardiomyopathy, also known as CMD1CC. Alternatively spliced transcript variants have been described.[provided by RefSeq, Feb 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
PVS1
Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
PM2
Very rare variant in population databases, with high coverage;
BS2
High AC in GnomAdExome4 at 5 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEXN | NM_144573.4 | c.25_27+2del | splice_donor_variant, coding_sequence_variant | 2/13 | ENST00000334785.12 | NP_653174.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEXN | ENST00000334785.12 | c.25_27+2del | splice_donor_variant, coding_sequence_variant | 2/13 | 1 | NM_144573.4 | ENSP00000333938 | P3 | ||
NEXN | ENST00000401035.7 | c.25_27+2del | splice_donor_variant, coding_sequence_variant | 2/9 | 1 | ENSP00000383814 | ||||
NEXN | ENST00000330010.12 | c.25_27+2del | splice_donor_variant, coding_sequence_variant | 2/12 | 2 | ENSP00000327363 | A1 | |||
NEXN | ENST00000440324.5 | c.25_27+2del | splice_donor_variant, coding_sequence_variant | 2/10 | 5 | ENSP00000411902 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000818 AC: 2AN: 244582Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132640
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GnomAD4 exome AF: 0.00000344 AC: 5AN: 1452972Hom.: 0 AF XY: 0.00000277 AC XY: 2AN XY: 722790
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GnomAD4 genome Cov.: 32
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 09, 2023 | The c.25_27+2delGAGGT variant results from a deletion of 5 nucleotides between positions 25 and 27+2 and involves the canonical splice donor site after coding exon 1 of the NEXN gene. This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). The canonical splice donor site is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. Although biallelic loss of function alterations in NEXN have been associated with autosomal recessive NEXN-related cardiomyopathy, haploinsufficiency for NEXN has not been clearly established as a mechanism of disease for autosomal dominant NEXN-related cardiomyopathy. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at