rs1555607285
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4_SupportingPP5
The NM_022463.5(NXN):c.1234_1236del(p.Glu412del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 31)
Consequence
NXN
NM_022463.5 inframe_deletion
NM_022463.5 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.99
Genes affected
NXN (HGNC:18008): (nucleoredoxin) This gene encodes a member of the thioredoxin superfamily, a group of small, multifunctional redox-active proteins. Members of this family are characterized by a conserved active motif called the thioredoxin fold that catalyzes disulfide bond formation and isomerization. The encoded protein acts a redox-dependent regulator of the Wnt signaling pathway and is involved in cell growth and differentiation. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_022463.5. Strenght limited to Supporting due to length of the change: 1aa.
PP5
?
Variant 17-801020-TCTC-T is Pathogenic according to our data. Variant chr17-801020-TCTC-T is described in ClinVar as [Pathogenic]. Clinvar id is 488062.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr17-801020-TCTC-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NXN | NM_022463.5 | c.1234_1236del | p.Glu412del | inframe_deletion | 8/8 | ENST00000336868.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NXN | ENST00000336868.8 | c.1234_1236del | p.Glu412del | inframe_deletion | 8/8 | 1 | NM_022463.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 genomes
?
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 31
GnomAD4 genome
?
Cov.:
31
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Robinow syndrome, autosomal recessive 2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 08, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at