VCV000221619.4 - ClinVar

NM_014171.5(CRIPT):c.-422_17-582del

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.

(2)

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.

Pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_014171.5(CRIPT):c.-422_17-582del

Variation ID: 221619 Accession: VCV000221619.4

Type and length

Deletion, 1,331 bp

Location

Cytogenetic: 2p21 2: 46616861-46618191 (GRCh38) [ NCBI UCSC ] 2: 46844000-46845330 (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	Sep 17, 2016	May 7, 2024	Dec 23, 2015

HGVS

Nucleotide	Protein	Molecular consequence
NC_000002.12:g.46616861_46618191del
NC_000002.11:g.46844000_46845330del
NG_034144.1:g.4690_6020del

Protein change

Other names

EX1DEL

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

ClinGen: CA10575848 OMIM: 604594.0004 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.
CRIPT		-	-	GRCh38 GRCh37	74	94
PIGF		-	-	GRCh38 GRCh37	19	51

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.
Rothmund-Thomson syndrome, type 3	Pathogenic (2)	criteria provided, single submitter	Dec 23, 2015	RCV000240818.11

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.
Pathogenic (Dec 23, 2015)	criteria provided, single submitter (Submitter's publication) Method: clinical testing	Rothmund-Thomson syndrome, type 3 (Autosomal recessive inheritance) Affected status: yes Allele origin: paternal	Baylor Genetics Study: Clinical whole exome sequencing Accession: SCV000262607.1 First in ClinVar: Sep 17, 2016 Last updated: Sep 17, 2016	Publications: PubMed (1) PubMed: 27250922 Comment: This variant was found in compound heterozygous status with a missense in exon 1 in one affected individual. Number of individuals with the variant: 1 Zygosity: Compound Heterozygote Family history: no Age: 0-4 years Sex: female Ethnicity/Population group: African-American Geographic origin: United States Tissue: Blood
Pathogenic (Apr 29, 2024)	no assertion criteria provided Method: literature only	ROTHMUND-THOMSON SYNDROME, TYPE 3 Affected status: not provided Allele origin: germline	OMIM Accession: SCV000864239.2 First in ClinVar: Sep 17, 2016 Last updated: May 07, 2024	Publications: PubMed (1) PubMed: 27250922 Comment on evidence: For discussion of the 1.3-kb deletion on chromosome 2 (chr2: 46,844,000-46,845,330), encompassing exon 1 of the CRIPT gene as well as the untranslated exon 1 … (more) For discussion of the 1.3-kb deletion on chromosome 2 (chr2: 46,844,000-46,845,330), encompassing exon 1 of the CRIPT gene as well as the untranslated exon 1 of the PIGF gene (600153), that was found in compound heterozygous state in a 4-year-old African American girl with short stature, microcephaly, facial dysmorphism, and hyper- and hypopigmented skin (RTS3; 615789) by Leduc et al. (2016), see 604594.0003. (less)

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

Title	Author	Journal	Year	Link
CRIPT exonic deletion and a novel missense mutation in a female with short stature, dysmorphic features, microcephaly, and pigmentary abnormalities.	Leduc MS	American journal of medical genetics. Part A	2016	PMID: 27250922

Text-mined citations for this variant ...

Record last updated Feb 01, 2025

ClinVar Genomic variation as it relates to human health

NM_014171.5(CRIPT):c.-422_17-582del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...