rs387907374
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2PM5PP3_StrongPP5_Moderate
The NM_014585.6(SLC40A1):c.262A>G(p.Arg88Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,772 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R88T) has been classified as Likely pathogenic.
Frequency
Consequence
NM_014585.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC40A1 | NM_014585.6 | c.262A>G | p.Arg88Gly | missense_variant | 3/8 | ENST00000261024.7 | |
SLC40A1 | XM_047444066.1 | c.142A>G | p.Arg48Gly | missense_variant | 3/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC40A1 | ENST00000261024.7 | c.262A>G | p.Arg88Gly | missense_variant | 3/8 | 1 | NM_014585.6 | P1 | |
SLC40A1 | ENST00000479598.5 | n.543A>G | non_coding_transcript_exon_variant | 3/4 | 1 | ||||
SLC40A1 | ENST00000427241.5 | c.262A>G | p.Arg88Gly | missense_variant | 5/8 | 5 | |||
SLC40A1 | ENST00000418714.1 | n.703A>G | non_coding_transcript_exon_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461772Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727192
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Hemochromatosis type 4 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Laboratory of Molecular Genetics and Genomics, Rennes University Hospital | Jul 01, 2020 | - - |
not provided Other:1
not provided, no classification provided | literature only | Laboratoire de Génétique Moléculaire, CHU Pontchaillou | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at