chr4-25662705-CA-C
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_ModeratePM2PP5
The ENST00000503434.5(SLC34A2):c.113-2del variant causes a splice acceptor change. The variant was absent in control chromosomes in GnomAD project. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 31)
Consequence
SLC34A2
ENST00000503434.5 splice_acceptor
ENST00000503434.5 splice_acceptor
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.78
Genes affected
SLC34A2 (HGNC:11020): (solute carrier family 34 member 2) The protein encoded by this gene is a pH-sensitive sodium-dependent phosphate transporter. Phosphate uptake is increased at lower pH. Defects in this gene are a cause of pulmonary alveolar microlithiasis. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PVS1
?
Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.0647343 fraction of the gene. Cryptic splice site detected, with MaxEntScore 9.8, offset of -2, new splice context is: accccttttgcttgtttcAGcga. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 4-25662705-CA-C is Pathogenic according to our data. Variant chr4-25662705-CA-C is described in ClinVar as [Pathogenic]. Clinvar id is 5715.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC34A2 | NM_006424.3 | c.114del | p.Asp39IlefsTer7 | frameshift_variant, splice_region_variant | 3/13 | ENST00000382051.8 | |
SLC34A2 | NM_001177998.2 | c.113-2del | splice_acceptor_variant | ||||
SLC34A2 | NM_001177999.2 | c.113-2del | splice_acceptor_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC34A2 | ENST00000382051.8 | c.114del | p.Asp39IlefsTer7 | frameshift_variant, splice_region_variant | 3/13 | 1 | NM_006424.3 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 genomes
?
Cov.:
31
GnomAD4 exome Cov.: 33
GnomAD4 exome
Cov.:
33
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
PULMONARY ALVEOLAR MICROLITHIASIS Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 2006 | - - |
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
Publications
No publications associated with this variant yet.