rs386833796
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2PM4_SupportingPP5_Very_Strong
The NM_003982.4(SLC7A7):βc.106_108delβ(p.Glu36del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,868 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (β β ).
Frequency
Genomes: not found (cov: 32)
Exomes π: 0.0000027 ( 0 hom. )
Consequence
SLC7A7
NM_003982.4 inframe_deletion
NM_003982.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.02
Genes affected
SLC7A7 (HGNC:11065): (solute carrier family 7 member 7) The protein encoded by this gene is the light subunit of a cationic amino acid transporter. This sodium-independent transporter is formed when the light subunit encoded by this gene dimerizes with the heavy subunit transporter protein SLC3A2. This transporter is found in epithelial cell membranes where it transfers cationic and large neutral amino acids from the cell to the extracellular space. Defects in this gene are a cause of lysinuric protein intolerance (LPI). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2011]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_003982.4. Strenght limited to Supporting due to length of the change: 1aa.
PP5
Variant 14-22813290-TCTC-T is Pathogenic according to our data. Variant chr14-22813290-TCTC-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 56348.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-22813290-TCTC-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC7A7 | NM_003982.4 | c.106_108del | p.Glu36del | inframe_deletion | 2/10 | ENST00000674313.1 | NP_003973.3 | |
SLC7A7 | NM_001126105.3 | c.106_108del | p.Glu36del | inframe_deletion | 3/11 | NP_001119577.1 | ||
SLC7A7 | NM_001126106.4 | c.106_108del | p.Glu36del | inframe_deletion | 3/11 | NP_001119578.1 | ||
SLC7A7 | XM_011537299.2 | c.106_108del | p.Glu36del | inframe_deletion | 2/10 | XP_011535601.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC7A7 | ENST00000674313.1 | c.106_108del | p.Glu36del | inframe_deletion | 2/10 | NM_003982.4 | ENSP00000501493 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461868Hom.: 0 AF XY: 0.00000275 AC XY: 2AN XY: 727242
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
Bravo
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ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Lysinuric protein intolerance Pathogenic:3
Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Feb 12, 2024 | - - |
Likely pathogenic, no assertion criteria provided | literature only | Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) | - | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 14, 2022 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at