chrX:77276563:A>G Detail (hg19) (ATP7A, PGK1)

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

Information

Genome

Assembly	Position
hg19	chrX:77,276,563-77,276,563
hg38	chrX:78,021,066-78,021,066 View the variant detail on this assembly version.

HGVS

ATP7A
PGK1

Type	Transcript	Protein
RefSeq	NM_000052.6:c.2903A>G	NP_000043.4:p.Glu968Gly
	NM_001282224.1:c.2933A>G	NP_001269153.1:p.Glu978Gly
Ensemble	ENST00000341514.11:c.2903A>G	ENST00000341514.11:p.Glu968Gly
	ENST00000343533.10:c.2933A>G	ENST00000343533.10:p.Glu978Gly
	ENST00000685264.1:c.2903A>G	ENST00000685264.1:p.Glu968Gly
	ENST00000686033.1:c.2903A>G	ENST00000686033.1:p.Glu968Gly
	ENST00000686133.1:c.2903A>G	ENST00000686133.1:p.Glu968Gly
	ENST00000686543.1:c.2669A>G	ENST00000686543.1:p.Glu890Gly
	ENST00000687086.1:c.2903A>G	ENST00000687086.1:p.Glu968Gly
	ENST00000689767.1:c.2996A>G	ENST00000689767.1:p.Glu999Gly
	ENST00000692908.1:c.2669A>G	ENST00000692908.1:p.Glu890Gly

Type	Transcript	Protein
RefSeq
Ensemble	ENST00000644362.1:c.-19-88801A>G

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	Conflicting classifications of pathogenicity
Review star
Show details

Links

ATP7A
PGK1

Type	Database	ID	Link
Gene	MIM	300011	OMIM
	HGNC	869	HGNC
	Ensembl	ENSG00000165240	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar
	COSMIC
	MONDO

Type	Database	ID	Link
Gene	MIM	311800	OMIM
	HGNC	8896	HGNC
	Ensembl	ENSG00000102144	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
Benign	2023-08-22	criteria provided, single submitter	Menkes kinky-hair syndrome	germline	Detail
Conflicting interpretations of pathogenicity	2019-08-26	criteria provided, conflicting interpretations	not provided	germline	Detail
Likely benign	2019-02-15	criteria provided, single submitter	not specified	germline	Detail
Benign	2024-01-18	criteria provided, single submitter	Cutis laxa, X-linked,Menkes kinky-hair syndrome,X-linked distal spinal muscular atrophy type 3	germline	Detail
Benign	2024-01-18	criteria provided, single submitter	Cutis laxa, X-linked,Menkes kinky-hair syndrome,X-linked distal spinal muscular atrophy type 3	germline	Detail
Benign	2024-01-18	criteria provided, single submitter	Cutis laxa, X-linked,Menkes kinky-hair syndrome,X-linked distal spinal muscular atrophy type 3	germline	Detail
Likely benign	2020-11-19	criteria provided, single submitter	Ehlers-Danlos syndrome	germline	Detail
Benign	2017-12-18	criteria provided, single submitter	Inborn genetic diseases	germline	Detail
Benign	2020-12-21	criteria provided, single submitter	ATP7A-related disorder	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.606	Menkes Kinky Hair Syndrome	NA	CLINVAR		Detail

Annotation

Annotations

Descrption	Source	Links
NM_000052.7(ATP7A):c.2903A>G (p.Glu968Gly) AND Menkes kinky-hair syndrome	ClinVar	Detail
NM_000052.7(ATP7A):c.2903A>G (p.Glu968Gly) AND not provided	ClinVar	Detail
NM_000052.7(ATP7A):c.2903A>G (p.Glu968Gly) AND not specified	ClinVar	Detail
NM_000052.7(ATP7A):c.2903A>G (p.Glu968Gly) AND multiple conditions	ClinVar	Detail
NM_000052.7(ATP7A):c.2903A>G (p.Glu968Gly) AND multiple conditions	ClinVar	Detail
NM_000052.7(ATP7A):c.2903A>G (p.Glu968Gly) AND multiple conditions	ClinVar	Detail
NM_000052.7(ATP7A):c.2903A>G (p.Glu968Gly) AND Ehlers-Danlos syndrome	ClinVar	Detail
NM_000052.7(ATP7A):c.2903A>G (p.Glu968Gly) AND Inborn genetic diseases	ClinVar	Detail
NM_000052.7(ATP7A):c.2903A>G (p.Glu968Gly) AND ATP7A-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: rs138958687 dbSNP
Genome: hg19
Position: chrX:77,276,563-77,276,563
Variant Type: snv
Reference Allele: A
Alternative Allele: G
East Asian Chromosome Counts (ExAC): 6630
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): 87641
Allele Counts in All Race (ExAC): 60
Heterozygous Counts in All Race (ExAC): 32
Homozygous Counts in All Race (ExAC): 0
Allele Frequency in All Race (ExAC): 6.846110838534476E-4
East Asian Hemizygous Counts (ExAC): 0
Hemizygous Counts in All Race (ExAC): 28

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