chr16:89550502:A>T Detail (hg38) (SPG7)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
Genome browser

Information

Genome

Assembly	Position
hg19	chr16:89,616,910-89,616,910 View the variant detail on this assembly version.
hg38	chr16:89,550,502-89,550,502

HGVS

SPG7

Type	Transcript	Protein
RefSeq	NM_003119.3:c.1651A>T	NP_003110.1:p.Lys551Ter
Ensemble	ENST00000268704.7:c.1651A>T	ENST00000268704.7:p.Lys551Ter
	ENST00000643649.1:c.1561A>T	ENST00000643649.1:p.Lys521Ter
	ENST00000644781.1:c.1672A>T	ENST00000644781.1:p.Lys558Ter
	ENST00000645063.1:c.1672A>T	ENST00000645063.1:p.Lys558Ter
	ENST00000645818.2:c.1672A>T	ENST00000645818.2:p.Lys558Ter
	ENST00000645897.1:c.1210A>T	ENST00000645897.1:p.Lys404Ter
	ENST00000646303.1:c.1540A>T	ENST00000646303.1:p.Lys514Ter
	ENST00000646716.1:c.724A>T	ENST00000646716.1:p.Lys242Ter
	ENST00000647079.1:c.1264A>T	ENST00000647079.1:p.Lys422Ter

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

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

Prediction

ClinVar

Clinical Significance	Pathogenic
Review star
Show details

Links

SPG7

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
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Pathogenic	2023-12-20	criteria provided, multiple submitters, no conflicts	hereditary spastic paraplegia 7	germline maternal paternal unknown	Detail
Pathogenic	2023-11-03	criteria provided, multiple submitters, no conflicts	not provided	germline unknown	Detail
Pathogenic	2017-04-07	no assertion criteria provided	Mitochondrial disease	germline	Detail
Pathogenic	2016-12-12	criteria provided, single submitter	hereditary spastic paraplegia	germline	Detail
Pathogenic	2022-08-17	criteria provided, single submitter	Inborn genetic diseases	germline	Detail
Pathogenic	2023-10-04	criteria provided, single submitter	SPG7-related disorder	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.560	SPASTIC PARAPLEGIA 7, AUTOSOMAL RECESSIVE	NA	CLINVAR		Detail

Annotation

Annotations

Descrption	Source	Links
NM_003119.4(SPG7):c.1672A>T (p.Lys558Ter) AND Hereditary spastic paraplegia 7	ClinVar	Detail
NM_003119.4(SPG7):c.1672A>T (p.Lys558Ter) AND not provided	ClinVar	Detail
NM_003119.4(SPG7):c.1672A>T (p.Lys558Ter) AND Mitochondrial disease	ClinVar	Detail
NM_003119.4(SPG7):c.1672A>T (p.Lys558Ter) AND Hereditary spastic paraplegia	ClinVar	Detail
NM_003119.4(SPG7):c.1672A>T (p.Lys558Ter) AND Inborn genetic diseases	ClinVar	Detail
NM_003119.4(SPG7):c.1672A>T (p.Lys558Ter) AND SPG7-related disorder	ClinVar	Detail
NA	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: rs369227537 dbSNP
Genome: hg38
Position: chr16:89,550,502-89,550,502
Variant Type: snv
Reference Allele: A
Alternative Allele: T
East Asian Chromosome Counts (ExAC): 8644
East Asian Allele Counts (ExAC): 0
East Asian Heterozygous Counts (ExAC): 0
East Asian Homozygous Counts (ExAC): 0
East Asian Allele Frequency (ExAC): 0.0
Chromosome Counts in All Race (ExAC): 121150
Allele Counts in All Race (ExAC): 17
Heterozygous Counts in All Race (ExAC): 17
Homozygous Counts in All Race (ExAC): 0
Allele Frequency in All Race (ExAC): 1.4032191498142797E-4

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