rs1060501102
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2PP3_StrongPP5_Very_Strong
The NM_014585.6(SLC40A1):c.1469G>A(p.Gly490Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Genomes: not found (cov: 33)
Consequence
SLC40A1
NM_014585.6 missense
NM_014585.6 missense
Scores
13
4
2
Clinical Significance
Conservation
PhyloP100: 7.91
Genes affected
SLC40A1 (HGNC:10909): (solute carrier family 40 member 1) The protein encoded by this gene is a cell membrane protein that may be involved in iron export from duodenal epithelial cells. Defects in this gene are a cause of hemochromatosis type 4 (HFE4). [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 14 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.98
PP5
Variant 2-189562125-C-T is Pathogenic according to our data. Variant chr2-189562125-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 406376.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Hemochromatosis type 4 Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Laboratory of Molecular Genetics and Genomics, Rennes University Hospital | Jul 01, 2020 | Identified in 11 patients harbouring clinical and biochemical symptomes of type 4 haemochromatosis - |
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 12, 2022 | This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 490 of the SLC40A1 protein (p.Gly490Asp). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with hyperferritinemia and iron overload (PMID: 12873829, 21199650, 24714983). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 406376). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). Experimental studies have shown that this missense change affects SLC40A1 function (PMID: 15692071, 15956209, 24714983). For these reasons, this variant has been classified as Pathogenic. - |
SLC40A1-related disorder Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 20, 2024 | The SLC40A1 c.1469G>A variant is predicted to result in the amino acid substitution p.Gly490Asp. This variant was reported in patients with hemochromatosis type 4 (Jouanelle et al. 2003. PubMed ID: 12873829; Rice et al. 2009. PubMed ID: 19150361; Le Gac et al. 2013. PubMed ID: 23784628; Callebaut et al. 2014. PubMed ID: 24714983). An in vitro study showed that this variant caused a loss of iron export function (Schimanski et al. 2005. PubMed ID: 15692071). Of note, another missense variant affecting the same amino acid (p.Gly490Ser) has also been reported as causative for hyperferritinemia (Callebaut et al. 2014. PubMed ID: 24714983). This variant has not been reported in a large population database, indicating this variant is rare. This variant is classified as pathogenic in ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/406376/). This variant is interpreted as pathogenic. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Pathogenic
D
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Pathogenic
D
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
M
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D
REVEL
Pathogenic
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MutPred
Gain of helix (P = 0.0199);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
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