NC_000023.10:g.(?_12885698)_(13787227_?)del AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 27, 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:: RCV003105403.2

Allele description

NC_000023.10:g.(?_12885698)_(13787227_?)del

Genes:

EGFL6:EGF like domain multiple 6 [Gene - OMIM - HGNC]
OFD1:OFD1 centriole and centriolar satellite protein [Gene - OMIM - HGNC]
RAB9A:RAB9A, member RAS oncogene family [Gene - OMIM - HGNC]
ATXN3L:ataxin 3 like [Gene - OMIM - HGNC]
FAM9C:family with sequence similarity 9 member C [Gene - OMIM - HGNC]
TMSB4X:thymosin beta 4 X-linked [Gene - OMIM - HGNC]
TLR7:toll like receptor 7 [Gene - OMIM - HGNC]
TLR8:toll like receptor 8 [Gene - OMIM - HGNC]
TRAPPC2:trafficking protein particle complex subunit 2 [Gene - OMIM - HGNC]
TCEANC:transcription elongation factor A N-terminal and central domain containing [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xp22.2

Genomic location:

ChrX: 12885698 - 13787227 (on Assembly GRCh37)

Preferred name:

NC_000023.10:g.(?_12885698)_(13787227_?)del

HGVS:

NC_000023.10:g.(?_12885698)_(13787227_?)del

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003794436	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 27, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 11349230, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003794436

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 27, 2022)

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

The molecular basis of X-linked spondyloepiphyseal dysplasia tarda.

Gedeon AK, Tiller GE, Le Merrer M, Heuertz S, Tranebjaerg L, Chitayat D, Robertson S, Glass IA, Savarirayan R, Cole WG, Rimoin DL, Kousseff BG, Ohashi H, Zabel B, Munnich A, Gecz J, Mulley JC.

Am J Hum Genet. 2001 Jun;68(6):1386-97. Epub 2001 May 8.

PubMed [citation]

PMID:: 11349230
PMCID:: PMC1226125

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, SCV003794436.1

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

Description

A gross deletion of the genomic region encompassing the full coding sequence of the TRAPPC2 gene has been identified. Loss-of-function variants in TRAPPC2 are known to be pathogenic (PMID: 11349230). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with TRAPPC2-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	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 10, 2023

ClinVar

Relating variation to medicine