NC_000006.11:g.(?_107019871)_(110266416_?)del AND not provided

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 4, 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:: RCV003116782.2

Allele description

NC_000006.11:g.(?_107019871)_(110266416_?)del

Genes:

AFG1L:AFG1 like ATPase [Gene - OMIM - HGNC]
BEND3:BEN domain containing 3 [Gene - OMIM - HGNC]
CD164:CD164 molecule [Gene - OMIM - HGNC]
FIG4:FIG4 phosphoinositide 5-phosphatase [Gene - OMIM - HGNC]
SEC63:SEC63 homolog, protein translocation regulator [Gene - OMIM - HGNC]
SCML4:Scm polycomb group protein like 4 [Gene - HGNC]
AK9:adenylate kinase 9 [Gene - OMIM - HGNC]
ARMC2:armadillo repeat containing 2 [Gene - OMIM - HGNC]
CEP57L1:centrosomal protein 57 like 1 [Gene - HGNC]
PDSS2:decaprenyl diphosphate synthase subunit 2 [Gene - OMIM - HGNC]
FOXO3:forkhead box O3 [Gene - OMIM - HGNC]
QRSL1:glutaminyl-tRNA amidotransferase subunit QRSL1 [Gene - OMIM - HGNC]
MICAL1:microtubule associated monooxygenase, calponin and LIM domain containing 1 [Gene - OMIM - HGNC]
MTRES1:mitochondrial transcription rescue factor 1 [Gene - OMIM - HGNC]
NR2E1:nuclear receptor subfamily 2 group E member 1 [Gene - OMIM - HGNC]
OSTM1:osteoclastogenesis associated transmembrane protein 1 [Gene - OMIM - HGNC]
PPIL6:peptidylprolyl isomerase like 6 [Gene - HGNC]
RTN4IP1:reticulon 4 interacting protein 1 [Gene - OMIM - HGNC]
SESN1:sestrin 1 [Gene - OMIM - HGNC]
SOBP:sine oculis binding protein homolog [Gene - OMIM - HGNC]
SNX3:sorting nexin 3 [Gene - OMIM - HGNC]
SMPD2:sphingomyelin phosphodiesterase 2 [Gene - OMIM - HGNC]
ZBTB24:zinc finger and BTB domain containing 24 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

6q21

Genomic location:

Chr6: 107019871 - 110266416 (on Assembly GRCh37)

Preferred name:

NC_000006.11:g.(?_107019871)_(110266416_?)del

HGVS:

NC_000006.11:g.(?_107019871)_(110266416_?)del

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

Recent activity

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CNTNAP3 contactin associated protein family member 3 [Homo sapiens]
CNTNAP3 contactin associated protein family member 3 [Homo sapiens]
Gene ID:79937

Gene
PREDICTED: Mus musculus MLX interacting protein-like (Mlxipl), transcript varian...
PREDICTED: Mus musculus MLX interacting protein-like (Mlxipl), transcript variant X9, mRNA
gi|1720414505|ref|XM_030254741.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003795164	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 4, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003795164

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 4, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

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, SCV003795164.1

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

Description

A gross deletion of the genomic region encompassing the full coding sequence of the QRSL1 gene has been identified. The current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in QRSL1 cause disease. 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 QRSL1-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Feb 18, 2023

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