NM_004260.4(RECQL4):c.113C>A (p.Thr38Asn) AND Rothmund-Thomson syndrome type 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 31, 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:: RCV003444847.1

Allele description [Variation Report for NM_004260.4(RECQL4):c.113C>A (p.Thr38Asn)]

NM_004260.4(RECQL4):c.113C>A (p.Thr38Asn)

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.113C>A (p.Thr38Asn)

HGVS:

NC_000008.11:g.144517607G>T
NG_016430.2:g.5220C>A
NG_033083.1:g.4643G>T
NM_004260.3:c.113C>A
NM_004260.4:c.113C>AMANE SELECT
NP_004251.4:p.Thr38Asn
LRG_277t1:c.113C>A
LRG_277:g.5220C>A
LRG_277p1:p.Thr38Asn
NC_000008.10:g.145742991G>T
NG_016430.1:g.5220C>A

Protein change:

T38N

Links:

dbSNP: rs1348040384

NCBI 1000 Genomes Browser:

rs1348040384

Molecular consequence:

NM_004260.4:c.113C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Rothmund-Thomson syndrome type 2 (RTS2)
Identifiers:: MONDO: MONDO:0016369; MedGen: C5203410; OMIM: 268400

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004171527	St. Jude Molecular Pathology, St. Jude Children's Research Hospital	criteria provided, single submitter (St. Jude Assertion Criteria 2020)	Uncertain significance (Oct 31, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004171527

St. Jude Molecular Pathology, St. Jude Children's Research Hospital

criteria provided, single submitter

(St. Jude Assertion Criteria 2020)

Uncertain significance
(Oct 31, 2023)

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

Details of each submission

From St. Jude Molecular Pathology, St. Jude Children's Research Hospital, SCV004171527.1

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

Description

The RECQL4 c.113C>A (p.Thr38Asn) missense change has a maximum subpopulation frequency of 0.035% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). In silico tools predict a deleterious effect of this variant on protein function, but to our knowledge functional studies have not been performed. To our knowledge, this variant has not been reported in individuals with RECQL4-associated conditions. In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance.

#	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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