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NM_007129.5(ZIC2):c.1229_1234del (p.Lys410_His411del) AND Holoprosencephaly 5

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 1, 2018
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:
RCV000691712.2

Allele description [Variation Report for NM_007129.5(ZIC2):c.1229_1234del (p.Lys410_His411del)]

NM_007129.5(ZIC2):c.1229_1234del (p.Lys410_His411del)

Gene:
ZIC2:Zic family member 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
13q32.3
Genomic location:
Preferred name:
NM_007129.5(ZIC2):c.1229_1234del (p.Lys410_His411del)
HGVS:
  • NC_000013.11:g.99985099_99985104del
  • NG_007085.3:g.8344_8349del
  • NM_007129.5:c.1229_1234delMANE SELECT
  • NP_009060.2:p.Lys410_His411del
  • LRG_1157t1:c.1229_1234del
  • LRG_1157:g.8344_8349del
  • LRG_1157p1:p.Lys410_His411del
  • NC_000013.10:g.100637353_100637358del
  • NM_007129.3:c.1229_1234delAGCACA
Links:
dbSNP: rs1566405714
NCBI 1000 Genomes Browser:
rs1566405714
Molecular consequence:
  • NM_007129.5:c.1229_1234del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:
Holoprosencephaly 5 (HPE5)
Identifiers:
MONDO: MONDO:0012322; MedGen: C1864827; Orphanet: 2162; OMIM: 609637

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000819502Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely pathogenic
(Aug 1, 2018)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000819502.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant, c.1229_1234delAGCACA, results in the deletion of 2 amino acid(s) of the ZIC2 protein (p.Lys410_His411del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (ExAC no frequency). This variant has been observed to be de novo in an individual affected developmental delay, posterior ureteral valves, laryngomalacia, dysphagia, cardiac arrest, pyriform aperture stenosis with a central incisor, rhomboencephalosynapsis and absence of the posterior pituitary bright spot (Invitae). Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the deleted amino acids is currently unknown. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 23, 2022