chr16:89598369:G>A Detail (hg19) (SPG7)

Information

Genome

Assembly Position
hg19 chr16:89,598,369-89,598,369
hg38 chr16:89,531,961-89,531,961 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_199367.2:c.1045G>A NP_955399.1:p.Gly349Ser
NM_003119.3:c.1024G>A NP_003110.1:p.Gly342Ser
Ensemble ENST00000643649.1:c.1045G>A ENST00000643649.1:p.Gly349Ser
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

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

Prediction

ClinVar

Clinical Significance Pathogenic Likely pathogenic
Review star
Show details
Links
Type Database ID Link
Gene MIM 602783 OMIM
HGNC 11237 HGNC
Ensembl ENSG00000197912 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv56630881 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic Likely pathogenic 2024-01-11 criteria provided, multiple submitters, no conflicts hereditary spastic paraplegia 7 germline unknown Detail
Pathogenic Likely pathogenic 2023-12-01 criteria provided, multiple submitters, no conflicts not provided germline unknown Detail
Likely pathogenic 2019-02-01 criteria provided, single submitter hereditary spastic paraplegia germline Detail
Pathogenic 2021-05-27 criteria provided, single submitter Inborn genetic diseases germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.560 SPASTIC PARAPLEGIA 7, AUTOSOMAL RECESSIVE NA CLINVAR Detail
0.560 SPASTIC PARAPLEGIA 7, AUTOSOMAL RECESSIVE The yeast complementation assay thus can serve as a reliable system to distingui... UNIPROT 20186691 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_003119.4(SPG7):c.1045G>A (p.Gly349Ser) AND Hereditary spastic paraplegia 7 ClinVar Detail
NM_003119.4(SPG7):c.1045G>A (p.Gly349Ser) AND not provided ClinVar Detail
NM_003119.4(SPG7):c.1045G>A (p.Gly349Ser) AND Hereditary spastic paraplegia ClinVar Detail
NM_003119.4(SPG7):c.1045G>A (p.Gly349Ser) AND Inborn genetic diseases ClinVar Detail
NA DisGeNET Detail
The yeast complementation assay thus can serve as a reliable system to distinguish a pathogenic muta... 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
rs141659620 dbSNP
Genome
hg19
Position
chr16:89,598,369-89,598,369
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1201
Mean of sample read depth (HGVD)
50.43
Standard deviation of sample read depth (HGVD)
25.01
Number of reference allele (HGVD)
2400
Number of alternative allele (HGVD)
2
Allele Frequency (HGVD)
8.326394671107411E-4
Gene Symbol (HGVD)
SPG7
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))
rs141659620
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8602
East Asian Allele Counts (ExAC)
1
East Asian Heterozygous Counts (ExAC)
1
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
1.1625203441060219E-4
Chromosome Counts in All Race (ExAC)
120402
Allele Counts in All Race (ExAC)
103
Heterozygous Counts in All Race (ExAC)
103
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
8.554675171508778E-4
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