NM_001194998.2(CEP152):c.2777A>T (p.Glu926Val) AND Microcephaly 9, primary, autosomal recessive

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Jan 13, 2018
Review status:: criteria provided, conflicting classifications

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:: RCV000145617.11

Allele description [Variation Report for NM_001194998.2(CEP152):c.2777A>T (p.Glu926Val)]

NM_001194998.2(CEP152):c.2777A>T (p.Glu926Val)

Gene:

CEP152:centrosomal protein 152 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q21.1

Genomic location:

Preferred name:

NM_001194998.2(CEP152):c.2777A>T (p.Glu926Val)

HGVS:

NC_000015.10:g.48756471T>A
NG_027518.2:g.59676A>T
NM_001194998.2:c.2777A>TMANE SELECT
NM_014985.4:c.2777A>T
NP_001181927.1:p.Glu926Val
NP_055800.2:p.Glu926Val
NC_000015.9:g.49048668T>A
NG_027518.1:g.59676A>T
NM_001194998.1:c.2777A>T
NM_014985.3:c.2777A>T

Protein change:

E926V

Links:

dbSNP: rs117557829

NCBI 1000 Genomes Browser:

rs117557829

Molecular consequence:

NM_001194998.2:c.2777A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_014985.4:c.2777A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Microcephaly 9, primary, autosomal recessive
Identifiers:: MONDO: MONDO:0013923; MedGen: C3553886; Orphanet: 2512; OMIM: 614852

Recent activity

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calpain-3 isoform X4 [Prionailurus viverrinus]
calpain-3 isoform X4 [Prionailurus viverrinus]
gi|2228843756|ref|XP_047718814.1|

Protein
PREDICTED: Homo sapiens epithelial cell transforming 2 (ECT2), transcript varian...
PREDICTED: Homo sapiens epithelial cell transforming 2 (ECT2), transcript variant X28, mRNA
gi|2462587797|ref|XM_054345559.1|

Nucleotide
hypothetical protein HMP0015_0162 [Acinetobacter haemolyticus ATCC 19194]
hypothetical protein HMP0015_0162 [Acinetobacter haemolyticus ATCC 19194]
gi|292825637|gb|EFF84361.1||gnl|WGS |HMP0015_0162

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000192714	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2007)	Uncertain significance (Feb 8, 2013)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000392876	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Jan 13, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000192714

Genetic Services Laboratory, University of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2007)

Uncertain significance
(Feb 8, 2013)

germline

clinical testing

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

SCV000392876

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Jan 13, 2018)

germline

clinical testing

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

Citations

PubMed

ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee..

Genet Med. 2008 Apr;10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae.

PubMed [citation]

PMID:: 18414213

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000192714.1

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

#	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

From Illumina Laboratory Services, Illumina, SCV000392876.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

#	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: Nov 10, 2024

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