NM_001353108.3(CEP63):c.1068-1G>A AND Seckel syndrome 6

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Jan 1, 2019
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:: RCV000194768.11

Allele description [Variation Report for NM_001353108.3(CEP63):c.1068-1G>A]

NM_001353108.3(CEP63):c.1068-1G>A

Gene:

CEP63:centrosomal protein 63 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q22.2

Genomic location:

Preferred name:

NM_001353108.3(CEP63):c.1068-1G>A

HGVS:

NC_000003.12:g.134549061G>A
NG_032870.1:g.68329G>A
NG_032870.2:g.68339G>A
NM_001042383.2:c.930-1G>A
NM_001042384.2:c.930-1G>A
NM_001042400.3:c.1068-1G>A
NM_001353108.3:c.1068-1G>AMANE SELECT
NM_001353109.1:c.930-1G>A
NM_001353110.1:c.1068-1G>A
NM_001353111.2:c.1068-1G>A
NM_001353112.2:c.1068-1G>A
NM_001353113.1:c.1068-1G>A
NM_001353117.2:c.1068-1G>A
NM_001353118.1:c.957-1G>A
NM_001353119.2:c.930-1G>A
NM_001353120.2:c.930-1G>A
NM_001353121.2:c.930-1G>A
NM_001353122.1:c.930-1G>A
NM_001353123.2:c.930-1G>A
NM_001353124.2:c.930-1G>A
NM_001353125.2:c.846-1G>A
NM_001353126.2:c.567-1G>A
NM_025180.5:c.1068-1G>A
NC_000003.11:g.134267903G>A
NM_001042383.1:c.930-1G>A
NM_025180.3:c.1068-1G>A
NM_025180.4:c.1068-1G>A

Links:

dbSNP: rs752207334

NCBI 1000 Genomes Browser:

rs752207334

Molecular consequence:

NM_001042383.2:c.930-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001042384.2:c.930-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001042400.3:c.1068-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001353108.3:c.1068-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001353109.1:c.930-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001353110.1:c.1068-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001353111.2:c.1068-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001353112.2:c.1068-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001353113.1:c.1068-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001353117.2:c.1068-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001353118.1:c.957-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001353119.2:c.930-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001353120.2:c.930-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001353121.2:c.930-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001353122.1:c.930-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001353123.2:c.930-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001353124.2:c.930-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001353125.2:c.846-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001353126.2:c.567-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_025180.5:c.1068-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Observations:

Condition(s)

Name:: Seckel syndrome 6 (SCKL6)
Identifiers:: MONDO: MONDO:0013871; MedGen: C3553582; OMIM: 614728

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000246999	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 27, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001432343	Service de Génétique Moléculaire, Hôpital Robert Debré	no assertion criteria provided	Pathogenic	unknown	clinical testing
SCV001440889	Institute of Human Genetics, University of Leipzig Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jan 1, 2019)	unknown	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

SCV000246999

Genetic Services Laboratory, University of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(May 27, 2015)

germline

clinical testing

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

SCV001432343

Service de Génétique Moléculaire, Hôpital Robert Debré

no assertion criteria provided

Pathogenic

unknown

clinical testing

SCV001440889

Institute of Human Genetics, University of Leipzig Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Jan 1, 2019)

unknown

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	unknown	yes	not provided	1	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000246999.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Service de Génétique Moléculaire, Hôpital Robert Debré, SCV001432343.1

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

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

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001440889.1

#	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	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 23, 2024

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