NM_001382391.1(CSPP1):c.3110-1G>A AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Sep 28, 2016
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:: RCV000483022.8

Allele description [Variation Report for NM_001382391.1(CSPP1):c.3110-1G>A]

NM_001382391.1(CSPP1):c.3110-1G>A

Genes:

ARFGEF1:ARF guanine nucleotide exchange factor 1 [Gene - OMIM - HGNC]
CSPP1:centrosome and spindle pole associated protein 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q13.2

Genomic location:

Preferred name:

NM_001382391.1(CSPP1):c.3110-1G>A

HGVS:

NC_000008.11:g.67177679G>A
NG_034100.1:g.118312G>A
NM_001291339.2:c.2060-1G>A
NM_001363131.2:c.3029-1G>A
NM_001363132.2:c.2915-1G>A
NM_001363133.2:c.2834-1G>A
NM_001364869.1:c.3176-1G>A
NM_001364870.1:c.2996-1G>A
NM_001382391.1:c.3110-1G>AMANE SELECT
NM_001413186.1:c.5368-2107C>T
NM_001413187.1:c.5386-2107C>T
NM_024790.6:c.3095-1G>A
NC_000008.10:g.68089914G>A

Links:

dbSNP: rs1064795687

NCBI 1000 Genomes Browser:

rs1064795687

Molecular consequence:

NM_001413186.1:c.5368-2107C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001413187.1:c.5386-2107C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001291339.2:c.2060-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001363131.2:c.3029-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001363132.2:c.2915-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001363133.2:c.2834-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001364869.1:c.3176-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001364870.1:c.2996-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001382391.1:c.3110-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_024790.6:c.3095-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000571717	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Sep 28, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000571717

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Sep 28, 2016)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000571717.3

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

Description

The c.3095-1G>A variant in the CSPP1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This splice site variant destroys the canonical splice acceptor site in intron 24. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. The c.3095-1G>A variant was not observed in approximately 5900 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The c.3095-1G>A variant is a strong candidate for a pathogenic variant.

#	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

Last Updated: Nov 3, 2024

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