NM_004260.4(RECQL4):c.84+1G>A AND Baller-Gerold syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Apr 12, 2023
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:: RCV001236750.5

Allele description [Variation Report for NM_004260.4(RECQL4):c.84+1G>A]

NM_004260.4(RECQL4):c.84+1G>A

Genes:

LOC130001411:ATAC-STARR-seq lymphoblastoid silent region 19699 [Gene]
RECQL4:RecQ like helicase 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q24.3

Genomic location:

Preferred name:

NM_004260.4(RECQL4):c.84+1G>A

HGVS:

NC_000008.11:g.144517700C>T
NG_016430.2:g.5127G>A
NG_033083.1:g.4736C>T
NG_033083.2:g.4710C>T
NG_180857.1:g.363C>T
NM_001413017.1:c.84+1G>A
NM_001413018.1:c.84+1G>A
NM_001413019.1:c.84+1G>A
NM_001413020.1:c.84+1G>A
NM_001413021.1:c.-701G>A
NM_001413022.1:c.-1052G>A
NM_001413023.1:c.-1052G>A
NM_001413024.1:c.-949G>A
NM_001413025.1:c.84+1G>A
NM_001413027.1:c.-1050+1G>A
NM_001413028.1:c.-777G>A
NM_001413029.1:c.84+1G>A
NM_001413030.1:c.-1114G>A
NM_001413031.1:c.-1114G>A
NM_001413032.1:c.-947+1G>A
NM_001413033.1:c.84+1G>A
NM_001413034.1:c.-956G>A
NM_001413035.1:c.-885+1G>A
NM_001413036.1:c.84+1G>A
NM_001413037.1:c.-1052G>A
NM_001413038.1:c.-1052G>A
NM_001413039.1:c.84+1G>A
NM_001413040.1:c.-957G>A
NM_001413041.1:c.-1114G>A
NM_001413042.1:c.-1052G>A
NM_001413043.1:c.-1321G>A
NM_004260.4:c.84+1G>AMANE SELECT
LRG_277t1:c.84+1G>A
LRG_277:g.5127G>A
NC_000008.10:g.145743084C>T
NM_004260.3:c.84+1G>A

Links:

dbSNP: rs1815425378

NCBI 1000 Genomes Browser:

rs1815425378

Molecular consequence:

NM_001413021.1:c.-701G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413022.1:c.-1052G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413023.1:c.-1052G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413024.1:c.-949G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413028.1:c.-777G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413030.1:c.-1114G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413031.1:c.-1114G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413034.1:c.-956G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413037.1:c.-1052G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413038.1:c.-1052G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413040.1:c.-957G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413041.1:c.-1114G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413042.1:c.-1052G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413043.1:c.-1321G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413017.1:c.84+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001413018.1:c.84+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001413019.1:c.84+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001413020.1:c.84+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001413025.1:c.84+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001413027.1:c.-1050+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001413029.1:c.84+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001413032.1:c.-947+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001413033.1:c.84+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001413035.1:c.-885+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001413036.1:c.84+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001413039.1:c.84+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_004260.4:c.84+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: Baller-Gerold syndrome (BGS)
Synonyms:: Craniosynostosis radial aplasia syndrome; Craniosynostosis with radial defects
Identifiers:: MONDO: MONDO:0009039; MedGen: C0265308; Orphanet: 1225; OMIM: 218600

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Gm9715 predicted gene 9715 [Mus musculus]
Gm9715 predicted gene 9715 [Mus musculus]
Gene ID:677423

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001409486	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Apr 12, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 16199547, 12734318, 12952869, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001409486

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Apr 12, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

Association between osteosarcoma and deleterious mutations in the RECQL4 gene in Rothmund-Thomson syndrome.

Wang LL, Gannavarapu A, Kozinetz CA, Levy ML, Lewis RA, Chintagumpala MM, Ruiz-Maldanado R, Contreras-Ruiz J, Cunniff C, Erickson RP, Lev D, Rogers M, Zackai EH, Plon SE.

J Natl Cancer Inst. 2003 May 7;95(9):669-74.

PubMed [citation]

PMID:: 12734318

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001409486.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 1 of the RECQL4 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in RECQL4 are known to be pathogenic (PMID: 12734318, 12952869). This variant has not been reported in the literature in individuals affected with RECQL4-related conditions. 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 962827).

#	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: Sep 29, 2024

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