VCV000152158.2 - ClinVar

GRCh38/hg38 Xp22.33-q28(chrX:251880-156004066)x1

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

conflicting data from submitters

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

GRCh38/hg38 Xp22.33-q28(chrX:251880-156004066)x1

Variation ID: 152158 Accession: VCV000152158.2

Type and length

copy number loss, 155,752,187 bp

Location

Cytogenetic: Xp22.33-q28 X: 251880-156004066 (GRCh38) [ NCBI UCSC ] X: 168547-155233731 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Oct 26, 2017	Oct 26, 2017	Mar 10, 2016

HGVS

Nucleotide	Protein	Molecular consequence
NC_000023.11:g.(?_251880)_(156004066_?)del
NC_000023.10:g.(?_168547)_(155233731_?)del

Protein change

Other names

Canonical SPDI

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

dbVar: nssv13638583 dbVar: nssv13638633 dbVar: nssv13640972 dbVar: nssv13645107 dbVar: nssv13645905 dbVar: nssv13647446 dbVar: nssv13649393 dbVar: nssv13650046 dbVar: nssv13652044 dbVar: nssv13656117 dbVar: nssv14081943 dbVar: nssv14082017 dbVar: nssv14082185 dbVar: nssv3395400 dbVar: nssv3397024 dbVar: nssv3397316 dbVar: nsv932069 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
PLP1		Sufficient evidence for dosage pathogenicity	Sufficient evidence for dosage pathogenicity	GRCh38 GRCh37	17	609
EFNB1		Sufficient evidence for dosage pathogenicity	Little evidence for dosage pathogenicity	GRCh38 GRCh37	154	289
ABCD1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	1524	1770
AFF2		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	300	497
ANOS1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	284	514
AP1S2		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	66	252
AR		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	820	1034
ARHGEF9		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	443	576
ARSL		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	427	666
ARX		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	692	1021

There are 2625 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh38 , GRCh37) and ClinGen Dosage Sensitivity Map.

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
See cases	conflicting data from submitters (1)	no assertion criteria provided	Mar 10, 2016	RCV000140787.7

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
conflicting data from submitters (Mar 10, 2016)	no assertion criteria provided Method: clinical testing	See cases Affected status: yes Allele origin: unknown	ISCA site 1 Additional submitter: International Standards For Cytogenomic Arrays Consortium (ISCA) Accession: SCV000181554.4 First in ClinVar: Aug 30, 2014 Last updated: Oct 26, 2017 Comments (2): Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations, with clinical assertions as classified by the original submitter. Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations, with clinical assertions as classified by the original submitter. For … (more) Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations, with clinical assertions as classified by the original submitter. For data from the original published study, [Kaminsky, et al. 2011\|/pubmed/21844811], please see [nstd101\|/dbvar/studies/nstd101/]. (less)	Publications: PubMed (1) PubMed: 20466091 Comment: Pathogenic(15), Uncertain significance(1) Observation 1: Number of individuals with the variant: 1 Clinical Features: Gonadal dysgenesis (present) , Abnormality of the face (present) Method: Microarray Result: Pass Observation 2: Number of individuals with the variant: 1 Clinical Features: Global developmental delay (present) Age: 0-9 years Sex: male Ethnicity/Population group: human Method: Microarray Result: Pass Observation 3: Number of individuals with the variant: 1 Clinical Features: Global developmental delay (present) , Short stature (present) Method: Microarray Result: Pass Observation 4: Number of individuals with the variant: 1 Clinical Features: Developmental delay AND/OR other significant developmental or morphological phenotypes (present) Method: Microarray Result: Pass Observation 5: Number of individuals with the variant: 1 Clinical Features: Micrognathia (present) , Failure to thrive (present) , Small for gestational age (present) , Coarctation of aorta (present) Method: Microarray Result: Pass Observation 6: Number of individuals with the variant: 1 Clinical Features: Oculomotor apraxia (present) , Ataxia (present) , Dysarthria (present) , Encephalopathy (present) Method: Microarray Result: Pass Observation 7: Number of individuals with the variant: 1 Clinical Features: Autism (present) , Muscular hypotonia (present) , Global developmental delay (present) , Attention deficit hyperactivity disorder (present) Method: Microarray Result: Pass Observation 8: Number of individuals with the variant: 1 Clinical Features: Developmental delay AND/OR other significant developmental or morphological phenotypes (present) Age: 0-9 years Sex: female Ethnicity/Population group: human Method: Microarray Result: Pass Observation 9: Number of individuals with the variant: 1 Clinical Features: Seizures (present) , Global developmental delay (present) Method: Microarray Result: Pass Observation 10: Number of individuals with the variant: 1 Clinical Features: Macroglossia (present) , Fibrous dysplasia of the bones (present) Method: Microarray Result: Pass Observation 11: Number of individuals with the variant: 1 Clinical Features: Respiratory distress (present) , Hypoplastic left heart (present) Method: Microarray Result: Pass Observation 12: Number of individuals with the variant: 1 Clinical Features: obsolete Malformation of the heart and great vessels (present) Sex: female Ethnicity/Population group: human Method: Microarray Result: Pass Observation 13: Number of individuals with the variant: 1 Clinical Features: Gonadal dysgenesis (present) , Abnormal facial shape (present) Age: 0-9 years Sex: female Ethnicity/Population group: human Method: Microarray Result: Pass Observation 14: Number of individuals with the variant: 1 Clinical Features: Failure to thrive (present) Method: Microarray Result: Pass Observation 15: Number of individuals with the variant: 1 Clinical Features: Delayed speech and language development (present) , Global developmental delay (present) , Short stature (present) Method: Microarray Result: Pass Observation 16: Number of individuals with the variant: 1 Clinical Features: Cleft palate (present) , Abnormality of the head (present) , Global developmental delay (present) Method: Microarray Result: Pass

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Sep 01, 2024

ClinVar Genomic variation as it relates to human health

GRCh38/hg38 Xp22.33-q28(chrX:251880-156004066)x1

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...