rs121918367
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3PP5
The NM_000617.3(SLC11A2):c.635G>T(p.Gly212Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000564 in 1,613,804 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 Pathogenic (no stars).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000055 ( 0 hom. )
Consequence
SLC11A2
NM_000617.3 missense
NM_000617.3 missense
Scores
7
4
7
Clinical Significance
Conservation
PhyloP100: 5.83
Genes affected
SLC11A2 (HGNC:10908): (solute carrier family 11 member 2) This gene encodes a member of the solute carrier family 11 protein family. The product of this gene transports divalent metals and is involved in iron absorption. Mutations in this gene are associated with hypochromic microcytic anemia with iron overload. A related solute carrier family 11 protein gene is located on chromosome 2. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Apr 2010]
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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;
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.803
PP5
?
Variant 12-50999214-C-A is Pathogenic according to our data. Variant chr12-50999214-C-A is described in ClinVar as [Pathogenic]. Clinvar id is 9078.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC11A2 | NM_000617.3 | c.635G>T | p.Gly212Val | missense_variant | 8/16 | ENST00000262052.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC11A2 | ENST00000262052.9 | c.635G>T | p.Gly212Val | missense_variant | 8/16 | 1 | NM_000617.3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 151938Hom.: 0 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251418Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135882
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GnomAD4 exome AF: 0.0000554 AC: 81AN: 1461866Hom.: 0 Cov.: 32 AF XY: 0.0000633 AC XY: 46AN XY: 727236
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GnomAD4 genome ? AF: 0.0000658 AC: 10AN: 151938Hom.: 0 Cov.: 32 AF XY: 0.0000405 AC XY: 3AN XY: 74154
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Microcytic anemia with liver iron overload Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 15, 2006 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
D;D;.;D;.;.;.;.;.;.;.;T;T
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
M_CAP
Benign
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;.;L;L;L;.;L;.;.;.;.;.
MutationTaster
Benign
A;A;A;A;A;A;A;A
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;.;.;D;D;.;D;D;D;D;D;D;D
REVEL
Uncertain
Sift
Benign
T;.;.;T;T;.;T;T;T;T;T;T;T
Sift4G
Benign
T;.;.;T;T;.;T;T;T;T;T;.;T
Polyphen
P;P;.;P;P;P;P;P;.;.;P;.;.
Vest4
MutPred
Gain of catalytic residue at T216 (P = 0.0117);Gain of catalytic residue at T216 (P = 0.0117);.;Gain of catalytic residue at T216 (P = 0.0117);Gain of catalytic residue at T216 (P = 0.0117);Gain of catalytic residue at T216 (P = 0.0117);.;Gain of catalytic residue at T216 (P = 0.0117);.;.;.;.;.;
MVP
MPC
1.4
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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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