chr19:40902308:C>T Detail (hg19) (PRX)

Information

Genome

Assembly Position
hg19 chr19:40,902,308-40,902,308
hg38 chr19:40,396,401-40,396,401 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_181882.2:c.1951G>A NP_870998.2:p.Asp651Asn
NM_020956.2:c.*2156G>A
Ensemble ENST00000324001.8:c.1951G>A ENST00000324001.8:p.Asp651Asn
Summary

MGeND

Clinical significance Pathogenic
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.004
ToMMo:0.006
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Uncertain significance
Review star
Show details
Links
Type Database ID Link
Gene MIM 605725 OMIM
HGNC 13797 HGNC
Ensembl ENSG00000105227 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv62093921 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic other germline MGS000001
(TMGS000174) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2012-11-01 no assertion criteria provided Charcot-Marie-Tooth disease type 4F germline unknown Detail
not provided no assertion provided not provided not provided Detail
Uncertain significance 2021-08-27 criteria provided, single submitter Charcot-Marie-Tooth disease type 4 germline Detail
Uncertain significance no assertion criteria provided Charcot-Marie-Tooth disease germline Detail
Uncertain significance 2021-07-13 criteria provided, single submitter Inborn genetic diseases germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.360 CHARCOT-MARIE-TOOTH DISEASE, DEMYELINATING, TYPE 4F NA CLINVAR Detail
0.360 CHARCOT-MARIE-TOOTH DISEASE, DEMYELINATING, TYPE 4F Late-onset Charcot-Marie-Tooth disease 4F caused by periaxin gene mutation. UNIPROT 22847150 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_181882.3(PRX):c.1951G>A (p.Asp651Asn) AND Charcot-Marie-Tooth disease type 4F ClinVar Detail
NM_181882.3(PRX):c.1951G>A (p.Asp651Asn) AND not provided ClinVar Detail
NM_181882.3(PRX):c.1951G>A (p.Asp651Asn) AND Charcot-Marie-Tooth disease type 4 ClinVar Detail
NM_181882.3(PRX):c.1951G>A (p.Asp651Asn) AND Charcot-Marie-Tooth disease ClinVar Detail
NM_181882.3(PRX):c.1951G>A (p.Asp651Asn) AND Inborn genetic diseases ClinVar Detail
NA DisGeNET Detail
Late-onset Charcot-Marie-Tooth disease 4F caused by periaxin gene mutation. DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs3814290 dbSNP
Genome
hg19
Position
chr19:40,902,308-40,902,308
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
253.80
Standard deviation of sample read depth (HGVD)
125.03
Number of reference allele (HGVD)
2411
Number of alternative allele (HGVD)
9
Allele Frequency (HGVD)
0.00371900826446281
Gene Symbol (HGVD)
PRX
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs3814290
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0064
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
107
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8650
East Asian Allele Counts (ExAC)
1
East Asian Heterozygous Counts (ExAC)
1
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
1.1560693641618497E-4
Chromosome Counts in All Race (ExAC)
120776
Allele Counts in All Race (ExAC)
13
Heterozygous Counts in All Race (ExAC)
13
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
1.0763727892958865E-4
Genome browser