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GRCh38/hg38 1p36.12(chr1:21999190-22063093) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 23, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003448618.1

Allele description [Variation Report for GRCh38/hg38 1p36.12(chr1:21999190-22063093)]

GRCh38/hg38 1p36.12(chr1:21999190-22063093)

Genes:
  • LOC129929630:ATAC-STARR-seq lymphoblastoid active region 345 [Gene]
  • LOC129929633:ATAC-STARR-seq lymphoblastoid active region 347 [Gene]
  • LOC129929631:ATAC-STARR-seq lymphoblastoid silent region 392 [Gene]
  • LOC129929632:ATAC-STARR-seq lymphoblastoid silent region 393 [Gene]
  • LOC129929634:ATAC-STARR-seq lymphoblastoid silent region 394 [Gene]
  • LOC132088665:Neanderthal introgressed variant-containing enhancer experimental_5374 [Gene]
  • LOC120893122:Sharpr-MPRA regulatory region 3950 [Gene]
  • CDC42:cell division cycle 42 [Gene - OMIM - HGNC]
  • CELA3A:chymotrypsin like elastase 3A [Gene - OMIM - HGNC]
  • LINC01635:long intergenic non-protein coding RNA 1635 [Gene - HGNC]
  • LINC00339:long intergenic non-protein coding RNA 339 [Gene - HGNC]
Variant type:
copy number gain
Cytogenetic location:
1p36.12
Genomic location:
Chr1: 21999190 - 22063093 (on Assembly GRCh38)
Preferred name:
GRCh38/hg38 1p36.12(chr1:21999190-22063093)
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004176160New York Genome Center
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Uncertain significance
(Aug 23, 2023) 		inheritedclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedinheritedunknown1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center, SCV004176160.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The inherited 1p36.12 duplication contains 5 genes, 2 MIM associated genes and partially contains one MIM disease associated gene, CDC42. Only the first exon of CDC42 (exon 1 of 6), which is a non-coding exon is contained within this duplication. Similar duplications of this region including exon 1 of CDC42 are not reported in population databases (gnomAD SVs, Database of Genomic Variants), suggesting it is not a common benign variant in the populations represented in those databases. This exact duplication is absent from ClinVar and to our current knowledge has not been reported in affected individuals in the literature. Given the lack of compelling evidence for its pathogenicity and the uncertain functional consequence of CDC42 exon 1 duplication, the inherited 1p36.12 duplication observed is reported as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedunknown1not providednot provided1not providednot providednot provided

Last Updated: Dec 17, 2023