NR_023343.3(RNU4ATAC):n.116A>G AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jan 18, 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:: RCV002555934.3

Allele description [Variation Report for NR_023343.3(RNU4ATAC):n.116A>G]

NR_023343.3(RNU4ATAC):n.116A>G

Genes:

RNU4ATAC:RNA, U4atac small nuclear [Gene - OMIM - HGNC]
CLASP1:cytoplasmic linker associated protein 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q14.2

Genomic location:

Preferred name:

NR_023343.3(RNU4ATAC):n.116A>G

HGVS:

NC_000002.12:g.121530995A>G
NG_029832.1:g.5116A>G
NM_001142273.2:c.196-670T>C
NM_001142274.2:c.196-670T>C
NM_001207051.2:c.196-670T>C
NM_001378003.1:c.196-670T>C
NM_001378004.1:c.196-670T>C
NM_001378005.1:c.196-670T>C
NM_001395891.1:c.196-670T>CMANE SELECT
NM_015282.3:c.196-670T>C
LRG_1202t1:n.116A>G
LRG_1202:g.5116A>G
NC_000002.11:g.122288571A>G
NC_000002.11:g.122288571A>G
NR_023343.1:n.116A>G
NR_023343.2:n.115A>G
NR_023343.3:n.116A>G

Links:

dbSNP: rs982261295

NCBI 1000 Genomes Browser:

rs982261295

Molecular consequence:

NM_001142273.2:c.196-670T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001142274.2:c.196-670T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001207051.2:c.196-670T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001378003.1:c.196-670T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001378004.1:c.196-670T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001378005.1:c.196-670T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001395891.1:c.196-670T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_015282.3:c.196-670T>C - intron variant - [Sequence Ontology: SO:0001627]

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
SCV003524680	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Jan 18, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 32628740, 30368667, 29263834, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003524680

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Jan 18, 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

Clinical interpretation of variants identified in RNU4ATAC, a non-coding spliceosomal gene.

Benoit-Pilven C, Besson A, Putoux A, Benetollo C, Saccaro C, Guguin J, Sala G, Cologne A, Delous M, Lesca G, Padgett RA, Leutenegger AL, Lacroix V, Edery P, Mazoyer S.

PLoS One. 2020;15(7):e0235655. doi: 10.1371/journal.pone.0235655.

PubMed [citation]

PMID:: 32628740
PMCID:: PMC7337319

Lowry-Wood syndrome: further evidence of association with RNU4ATAC, and correlation between genotype and phenotype.

Shelihan I, Ehresmann S, Magnani C, Forzano F, Baldo C, Brunetti-Pierri N, Campeau PM.

Hum Genet. 2018 Dec;137(11-12):905-909. doi: 10.1007/s00439-018-1950-8. Epub 2018 Oct 27.

PubMed [citation]

PMID:: 30368667

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003524680.2

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

Description

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. This variant is located within the Sm protein-binding region of the RNU4ATAC RNA, which is important for small nuclear RNA maturation (PMID: 32628740). A significant number of disease-associated RNU4ATAC variants are found in this region (PMID: 32628740, 30368667). ClinVar contains an entry for this variant (Variation ID: 870579). This variant has been observed in individual(s) with Roifman syndrome (PMID: 29263834; external communication). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (no rsID available, gnomAD 0.006%). This variant occurs in the RNU4ATAC gene, which encodes an RNA molecule that does not result in a protein product.

#	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: Oct 8, 2024

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