NC_000001.11:g.(?_155282411)_(155323834_?)del AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 21, 2019
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:: RCV000816636.4

Allele description [Variation Report for NC_000001.11:g.(?_155282411)_(155323834_?)del]

NC_000001.11:g.(?_155282411)_(155323834_?)del

Genes:

LOC129931559:ATAC-STARR-seq lymphoblastoid active region 1812 [Gene]
LOC129931560:ATAC-STARR-seq lymphoblastoid active region 1813 [Gene]
LOC129931561:ATAC-STARR-seq lymphoblastoid active region 1814 [Gene]
LOC129931562:ATAC-STARR-seq lymphoblastoid silent region 1400 [Gene]
LOC129931563:ATAC-STARR-seq lymphoblastoid silent region 1401 [Gene]
LOC129931564:ATAC-STARR-seq lymphoblastoid silent region 1402 [Gene]
LOC129931565:ATAC-STARR-seq lymphoblastoid silent region 1403 [Gene]
RUSC1:RUN and SH3 domain containing 1 [Gene - OMIM - HGNC]
RUSC1-AS1:RUSC1 antisense RNA 1 [Gene - HGNC]
FDPS:farnesyl diphosphate synthase [Gene - OMIM - HGNC]
HCN3:hyperpolarization activated cyclic nucleotide gated potassium channel 3 [Gene - OMIM - HGNC]
PKLR:pyruvate kinase L/R [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1q22

Genomic location:

Preferred name:

NC_000001.11:g.(?_155282411)_(155323834_?)del

HGVS:

NC_000001.11:g.(?_155282411)_(155323834_?)del
NC_000001.10:g.(?_155252202)_(155293625_?)del

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000957153	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 21, 2019)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 26202976, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000957153

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 21, 2019)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Genomic variations of the mevalonate pathway in porokeratosis.

Zhang Z, Li C, Wu F, Ma R, Luan J, Yang F, Liu W, Wang L, Zhang S, Liu Y, Gu J, Hua W, Fan M, Peng H, Meng X, Song N, Bi X, Gu C, Zhang Z, Huang Q, Chen L, Xiang L, et al.

Elife. 2015 Jul 23;4:e06322. doi: 10.7554/eLife.06322. Erratum in: Elife. 2016 Jan 27;5:e14383. doi: 10.7554/eLife.14383.

PubMed [citation]

PMID:: 26202976
PMCID:: PMC4511816

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000957153.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in FDPS are known to be pathogenic (PMID: 26202976). This variant has not been reported in the literature in individuals with FDPS-related disease. A gross deletion of the genomic region encompassing the full coding sequence of the FDPS gene has been identified. The boundaries of this event are unknown as the deletion extends beyond the assayed region for this gene and therefore may encompass additional genes.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 9, 2024

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