NM_003413.4(ZIC3):c.49G>T (p.Gly17Cys) AND VACTERL association, X-linked, with or without hydrocephalus

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Apr 28, 2017
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:: RCV000201846.10

Allele description [Variation Report for NM_003413.4(ZIC3):c.49G>T (p.Gly17Cys)]

NM_003413.4(ZIC3):c.49G>T (p.Gly17Cys)

Gene:

ZIC3:Zic family member 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq26.3

Genomic location:

Preferred name:

NM_003413.4(ZIC3):c.49G>T (p.Gly17Cys)

HGVS:

NC_000023.11:g.137566740G>T
NG_008115.2:g.5614G>T
NM_001330661.1:c.49G>T
NM_003413.4:c.49G>TMANE SELECT
NP_001317590.1:p.Gly17Cys
NP_003404.1:p.Gly17Cys
NC_000023.10:g.136648899G>T
NM_003413.3:c.49G>T
O60481:p.Gly17Cys

Protein change:

G17C

Links:

UniProtKB: O60481#VAR_071330; dbSNP: rs147232392

NCBI 1000 Genomes Browser:

rs147232392

Molecular consequence:

NM_001330661.1:c.49G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_003413.4:c.49G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: VACTERL association, X-linked, with or without hydrocephalus (VACTERLX)
Synonyms:: VACTERL-H, X-LINKED; VACTERL Association with Hydrocephalus, X-linked; VACTERL association with hydrocephaly, X-linked; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010752; MedGen: C2931228; Orphanet: 3412; OMIM: 314390

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000481807	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 28, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000481807

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 28, 2017)

germline

clinical testing

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

Citation Link

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
not provided	maternal	yes	4	3	not provided	not provided	yes	research

Citations

PubMed

[Characteristics of the formation of conditioned responses in the isolated LPa3 neuron of the edible snail].

Grechenko TN.

Zh Vyssh Nerv Deiat Im I P Pavlova. 1989 Nov-Dec;39(6):1170-2. Russian. No abstract available.

PubMed [citation]

PMID:: 2629409

Targeted Resequencing of 29 Candidate Genes and Mouse Expression Studies Implicate ZIC3 and FOXF1 in Human VATER/VACTERL Association.

Hilger AC, Halbritter J, Pennimpede T, van der Ven A, Sarma G, Braun DA, Porath JD, Kohl S, Hwang DY, Dworschak GC, Hermann BG, Pavlova A, El-Maarri O, Nöthen MM, Ludwig M, Reutter H, Hildebrandt F.

Hum Mutat. 2015 Dec;36(12):1150-4. doi: 10.1002/humu.22859. Epub 2015 Sep 14.

PubMed [citation]

PMID:: 26294094
PMCID:: PMC4643331

Details of each submission

From Reutter Lab, Institute of Human Genetics, University Hospital Bonn - Systematic search for genes to be involved in the VACTER/VACTERL association, SCV000222773.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	4	not provided	yes	research	PubMed (2)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	maternal	yes	not provided	not provided	not provided		4	not provided	3	not provided

From Illumina Laboratory Services, Illumina, SCV000481807.3

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#	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

Flagged submissions

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000222773	Reutter Lab, Institute of Human Genetics, University Hospital Bonn - Systematic search for genes to be involved in the VACTER/VACTERL association	flagged submission Reason: Outlier claim with insufficient supporting evidence Notes: None (Submitter's publication)	Pathogenic (Jan 1, 2015)	maternal	research	PubMed (2) [See all records that cite these PMIDs] 26294094, 2629409

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000222773

Reutter Lab, Institute of Human Genetics, University Hospital Bonn - Systematic search for genes to be involved in the VACTER/VACTERL association

flagged submission

Reason: Outlier claim with insufficient supporting evidence

Notes: None

(Submitter's publication)

Pathogenic
(Jan 1, 2015)

maternal

research

PubMed (2)
[See all records that cite these PMIDs]

Last Updated: Oct 20, 2024

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