rs549932754
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The ENST00000555633.3(RAX2):c.417_422del(p.Pro140_Gly141del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000131 in 1,530,990 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 7.3e-7 ( 0 hom. )
Consequence
RAX2
ENST00000555633.3 inframe_deletion
ENST00000555633.3 inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.48
Genes affected
RAX2 (HGNC:18286): (retina and anterior neural fold homeobox 2) This gene encodes a homeodomain-containing protein that plays a role in eye development. Mutation of this gene causes age-related macular degeneration type 6, an eye disorder resulting in accumulations of protein and lipid beneath the retinal pigment epithelium and within the Bruch's membrane. Defects in this gene can also cause cone-rod dystrophy type 11, a disease characterized by the initial degeneration of cone photoreceptor cells and resulting in loss of color vision and visual acuity, followed by the degeneration of rod photoreceptor cells, which progresses to night blindness and the loss of peripheral vision. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
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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 ENST00000555633.3.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAX2 | NM_001319074.4 | c.417_422del | p.Pro140_Gly141del | inframe_deletion | 3/3 | ENST00000555633.3 | NP_001306003.2 | |
RAX2 | NM_032753.4 | c.417_422del | p.Pro140_Gly141del | inframe_deletion | 3/3 | NP_116142.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAX2 | ENST00000555633.3 | c.417_422del | p.Pro140_Gly141del | inframe_deletion | 3/3 | 1 | NM_001319074.4 | ENSP00000450456 | P1 | |
RAX2 | ENST00000555978.5 | c.417_422del | p.Pro140_Gly141del | inframe_deletion | 3/3 | 1 | ENSP00000450687 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152196Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 7.25e-7 AC: 1AN: 1378794Hom.: 0 AF XY: 0.00000147 AC XY: 1AN XY: 680382
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74346
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at