NC_000017.10:g.(?_54671585)_(55927371_?)del AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 19, 2022
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:: RCV004581399.2

Allele description [Variation Report for NC_000017.10:g.(?_54671585)_(55927371_?)del]

NC_000017.10:g.(?_54671585)_(55927371_?)del

Genes:

AKAP1:A-kinase anchoring protein 1 [Gene - OMIM - HGNC]
C17orf67:chromosome 17 open reading frame 67 [Gene - HGNC]
COIL:coilin [Gene - OMIM - HGNC]
DGKE:diacylglycerol kinase epsilon [Gene - OMIM - HGNC]
MRPS23:mitochondrial ribosomal protein S23 [Gene - OMIM - HGNC]
MSI2:musashi RNA binding protein 2 [Gene - OMIM - HGNC]
NOG:noggin [Gene - OMIM - HGNC]
SCPEP1:serine carboxypeptidase 1 [Gene - OMIM - HGNC]
TRIM25:tripartite motif containing 25 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17q22

Genomic location:

Chr17: 54671585 - 55927371 (on Assembly GRCh37)

Preferred name:

NC_000017.10:g.(?_54671585)_(55927371_?)del

HGVS:

NC_000017.10:g.(?_54671585)_(55927371_?)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
SCV005066727	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 19, 2022)	unknown	clinical testing	PubMed (4) [See all records that cite these PMIDs] 31502745, 15699718, 31428484, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005066727

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 19, 2022)

unknown

clinical testing

PubMed (4)
[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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Multiplex targeted high-throughput sequencing in a series of 352 patients with congenital limb malformations.

Jourdain AS, Petit F, Odou MF, Balduyck M, Brunelle P, Dufour W, Boussion S, Brischoux-Boucher E, Colson C, Dieux A, Gérard M, Ghoumid J, Giuliano F, Goldenberg A, Khau Van Kien P, Lehalle D, Morin G, Moutton S, Smol T, Vanlerberghe C, Manouvrier-Hanu S, Escande F.

Hum Mutat. 2020 Jan;41(1):222-239. doi: 10.1002/humu.23912. Epub 2019 Sep 23.

PubMed [citation]

PMID:: 31502745

Teunissen-Cremers syndrome: a clinical, surgical, and genetic report.

Weekamp HH, Kremer H, Hoefsloot LH, Kuijpers-Jagtman AM, Cruysberg JR, Cremers CW.

Otol Neurotol. 2005 Jan;26(1):38-51.

PubMed [citation]

PMID:: 15699718

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV005066727.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. A similar copy number variant has been observed in individual(s) with congenital limb malformations (PMID: 31502745). A gross deletion of the genomic region encompassing the full coding sequence of the NOG gene has been identified. Loss-of-function variants in NOG are known to be pathogenic (PMID: 15699718, 31428484). The boundaries of this event are unknown as they extend 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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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