rs797045029
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PP3_ModeratePP5_Moderate
The NM_058172.6(ANTXR2):āc.241T>Cā(p.Ser81Pro) variant causes a missense change. The variant allele was found at a frequency of 0.000000689 in 1,451,090 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 (ā ).
Frequency
Genomes: not found (cov: 32)
Exomes š: 6.9e-7 ( 0 hom. )
Consequence
ANTXR2
NM_058172.6 missense
NM_058172.6 missense
Scores
10
6
2
Clinical Significance
Conservation
PhyloP100: 6.18
Genes affected
ANTXR2 (HGNC:21732): (ANTXR cell adhesion molecule 2) This gene encodes a receptor for anthrax toxin. The protein binds to collagen IV and laminin, suggesting that it may be involved in extracellular matrix adhesion. Mutations in this gene cause juvenile hyaline fibromatosis and infantile systemic hyalinosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
PM1
?
In a disulfide_bond (size 179) in uniprot entity ANTR2_HUMAN there are 11 pathogenic changes around while only 2 benign (85%) in NM_058172.6
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.902
PP5
?
Variant 4-80069491-A-G is Pathogenic according to our data. Variant chr4-80069491-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 209133.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANTXR2 | NM_058172.6 | c.241T>C | p.Ser81Pro | missense_variant | 3/17 | ENST00000403729.7 | |
ANTXR2 | NM_001145794.2 | c.241T>C | p.Ser81Pro | missense_variant | 3/16 | ||
ANTXR2 | NM_001286780.2 | c.10T>C | p.Ser4Pro | missense_variant | 3/17 | ||
ANTXR2 | NM_001286781.2 | c.10T>C | p.Ser4Pro | missense_variant | 3/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANTXR2 | ENST00000403729.7 | c.241T>C | p.Ser81Pro | missense_variant | 3/17 | 1 | NM_058172.6 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 6.89e-7 AC: 1AN: 1451090Hom.: 0 Cov.: 30 AF XY: 0.00000139 AC XY: 1AN XY: 720998
GnomAD4 exome
AF:
AC:
1
AN:
1451090
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
720998
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hyaline fibromatosis syndrome Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Jul 08, 2013 | At time of reporting, this variant was novel. Likely pathogenicity based on finding it in trans with a deleterious frameshift variant [T436fs] in a 21-year-old female with juvenile hyaline fibromatosis. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D;D;D;D
M_CAP
Benign
D
MetaRNN
Pathogenic
D;D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
M;.;M;M
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;D
REVEL
Pathogenic
Sift
Uncertain
D;D;D;D
Sift4G
Pathogenic
D;D;D;D
Polyphen
D;.;D;D
Vest4
MutPred
Gain of glycosylation at S81 (P = 0.0395);.;Gain of glycosylation at S81 (P = 0.0395);Gain of glycosylation at S81 (P = 0.0395);
MVP
MPC
0.67
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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