NC_000007.13:g.(?_152617597)_(158500659_?)del AND not provided

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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 29, 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:: RCV003122160.2

Allele description

NC_000007.13:g.(?_152617597)_(158500659_?)del

Genes:

HTR5A:5-hydroxytryptamine receptor 5A [Gene - OMIM - HGNC]
DNAJB6:DnaJ heat shock protein family (Hsp40) member B6 [Gene - OMIM - HGNC]
PAXIP1:PAX interacting protein 1 [Gene - OMIM - HGNC]
RBM33:RNA binding motif protein 33 [Gene - HGNC]
CNPY1:canopy FGF signaling regulator 1 [Gene - OMIM - HGNC]
EN2:engrailed homeobox 2 [Gene - OMIM - HGNC]
INSIG1:insulin induced gene 1 [Gene - OMIM - HGNC]
LMBR1:limb development membrane protein 1 [Gene - OMIM - HGNC]
MNX1:motor neuron and pancreas homeobox 1 [Gene - OMIM - HGNC]
NCAPG2:non-SMC condensin II complex subunit G2 [Gene - OMIM - HGNC]
NOM1:nucleolar protein with MIF4G domain 1 [Gene - OMIM - HGNC]
PTPRN2:protein tyrosine phosphatase receptor type N2 [Gene - OMIM - HGNC]
RNF32:ring finger protein 32 [Gene - OMIM - HGNC]
SHH:sonic hedgehog signaling molecule [Gene - OMIM - HGNC]
UBE3C:ubiquitin protein ligase E3C [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

7q36.2-36.3

Genomic location:

Chr7: 152617597 - 158500659 (on Assembly GRCh37)

Preferred name:

NC_000007.13:g.(?_152617597)_(158500659_?)del

HGVS:

NC_000007.13:g.(?_152617597)_(158500659_?)del

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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MULTISPECIES: alanyl-tRNA editing protein [Burkholderia]
MULTISPECIES: alanyl-tRNA editing protein [Burkholderia]
gi|490659265|ref|WP_004524255.1|

Protein
MULTISPECIES: alkaline phosphatase family protein [Burkholderia]
MULTISPECIES: alkaline phosphatase family protein [Burkholderia]
gi|490663633|ref|WP_004528623.1|

Protein
photosystem II protein T (chloroplast) [Pinus koraiensis]
photosystem II protein T (chloroplast) [Pinus koraiensis]
gi|29565630|ref|NP_817209.1|

Protein
Homo sapiens family with sequence similarity 26 member E (FAM26E), mRNA
Homo sapiens family with sequence similarity 26 member E (FAM26E), mRNA
gi|88196797|ref|NM_153711.2|

Nucleotide
clathrin coat assembly protein AP180 [Rattus norvegicus]
clathrin coat assembly protein AP180 [Rattus norvegicus]
gi|1941084626|ref|NP_113916.2|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003794820	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 29, 2022)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 10631160, 10749657, 16254195, 24095820, 23370340, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003794820

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 29, 2022)

germline

clinical testing

PubMed (6)
[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

Involvement of the HLXB9 homeobox gene in Currarino syndrome.

Belloni E, Martucciello G, Verderio D, Ponti E, Seri M, Jasonni V, Torre M, Ferrari M, Tsui LC, Scherer SW.

Am J Hum Genet. 2000 Jan;66(1):312-9. No abstract available.

PubMed [citation]

PMID:: 10631160
PMCID:: PMC1288336

Mutation analysis and embryonic expression of the HLXB9 Currarino syndrome gene.

Hagan DM, Ross AJ, Strachan T, Lynch SA, Ruiz-Perez V, Wang YM, Scambler P, Custard E, Reardon W, Hassan S, Nixon P, Papapetrou C, Winter RM, Edwards Y, Morrison K, Barrow M, Cordier-Alex MP, Correia P, Galvin-Parton PA, Gaskill S, Gaskin KJ, Garcia-Minaur S, et al.

Am J Hum Genet. 2000 May;66(5):1504-15. Epub 2000 Apr 4. Erratum in: Am J Hum Genet 2000 Sep;67(3):769.

PubMed [citation]

PMID:: 10749657
PMCID:: PMC1378009

See all PubMed Citations (6)

Details of each submission

From Invitae, SCV003794820.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the MNX1 gene has been identified. Loss-of-function variants in MNX1 are known to be pathogenic (PMID: 10631160, 10749657, 16254195, 24095820). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. A similar copy number variant has been observed in individual(s) with Currarino syndrome (PMID: 23370340). 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: Dec 9, 2023

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