NC_000004.11:g.(?_121616266)_(124323706_?)dup AND Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 22, 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:: RCV003113657.3

Allele description [Variation Report for NC_000004.11:g.(?_121616266)_(124323706_?)dup]

NC_000004.11:g.(?_121616266)_(124323706_?)dup

Genes:

AFG2A:AFG2 AAA ATPase homolog A [Gene - OMIM - HGNC]
BBS12:Bardet-Biedl syndrome 12 [Gene - OMIM - HGNC]
BBS7:Bardet-Biedl syndrome 7 [Gene - OMIM - HGNC]
PRDM5:PR/SET domain 5 [Gene - OMIM - HGNC]
TNIP3:TNFAIP3 interacting protein 3 [Gene - OMIM - HGNC]
ADAD1:adenosine deaminase domain containing 1 [Gene - OMIM - HGNC]
ANXA5:annexin A5 [Gene - OMIM - HGNC]
BLTP1:bridge-like lipid transfer protein family member 1 [Gene - OMIM - HGNC]
CCNA2:cyclin A2 [Gene - OMIM - HGNC]
EXOSC9:exosome component 9 [Gene - OMIM - HGNC]
FGF2:fibroblast growth factor 2 [Gene - OMIM - HGNC]
IL21:interleukin 21 [Gene - OMIM - HGNC]
IL2:interleukin 2 [Gene - OMIM - HGNC]
NDNF:neuron derived neurotrophic factor [Gene - OMIM - HGNC]
NUDT6:nudix hydrolase 6 [Gene - OMIM - HGNC]
QRFPR:pyroglutamylated RFamide peptide receptor [Gene - OMIM - HGNC]
SMIM43:small integral membrane protein 43 [Gene - HGNC]
SPRY1:sprouty RTK signaling antagonist 1 [Gene - OMIM - HGNC]
TRPC3:transient receptor potential cation channel subfamily C member 3 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

4q27-28.1

Genomic location:

Chr4: 121616266 - 124323706 (on Assembly GRCh37)

Preferred name:

NC_000004.11:g.(?_121616266)_(124323706_?)dup

HGVS:

NC_000004.11:g.(?_121616266)_(124323706_?)dup

Condition(s)

Name:: Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome (NEDHSB)
Synonyms:: NEURODEVELOPMENTAL DISORDER WITH HEARING LOSS, SEIZURES, AND BRAIN ABNORMALITIES
Identifiers:: MONDO: MONDO:0014698; MedGen: C4225276; Orphanet: 457351; OMIM: 616577

Recent activity

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Xenolepidichthys dalgleishi isolate #86 SH3 and PX domain-containing 3-like prot...
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gi|1381325721|gb|KY873979.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003796399	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 22, 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

SCV003796399

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 22, 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV003796399.2

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

Description

A copy number gain of the genomic region encompassing the full coding sequence of the SPATA5 gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals affected with SPATA5-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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: Sep 29, 2024

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