VCV001710082.2 - ClinVar

NM_001080449.3(DNA2):c.143T>C (p.Leu48Pro)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Likely pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001080449.3(DNA2):c.143T>C (p.Leu48Pro)

Variation ID: 1710082 Accession: VCV001710082.2

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 10q21.3 10: 68470095 (GRCh38) [ NCBI UCSC ] 10: 70229852 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Mar 26, 2023	May 12, 2024	Sep 22, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NM_001080449.3:c.143T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001073918.2:p.Leu48Pro	missense
NR_102264.2:n.232T>C		non-coding transcript variant
NC_000010.11:g.68470095A>G
NC_000010.10:g.70229852A>G
NG_034247.1:g.6879T>C

... more HGVS ... less HGVS

Protein change

L48P

Other names

Canonical SPDI

NC_000010.11:68470094:A:G

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

OMIM: 601810.0013 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
DNA2		-	-	GRCh38 GRCh37	-	-

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Rothmund-Thomson syndrome	Likely pathogenic (1)	criteria provided, single submitter	Sep 22, 2022	RCV003154242.2
Rothmund-Thomson syndrome, type 4	Pathogenic (1)	no assertion criteria provided	May 7, 2024	RCV004545281.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely pathogenic (Sep 22, 2022)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: research	Rothmund-Thomson syndrome (Autosomal recessive inheritance) Affected status: yes Allele origin: maternal	Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo Accession: SCV002581922.1 First in ClinVar: Mar 26, 2023 Last updated: Mar 26, 2023	Comment: Very rare variant, in-silico prediction of damage, in trans with the recurrent splicing variant in 1 proband with classic clinical presentation of Rothmund-Thomson Syndrome with … (more) Very rare variant, in-silico prediction of damage, in trans with the recurrent splicing variant in 1 proband with classic clinical presentation of Rothmund-Thomson Syndrome with congenital cataracts and severe growth restriction (DNA related RTS).Likely Pathogenic (PM2, PP3, PM3, PP4) (less) Clinical Features: Poikiloderma (present) , Developmental cataract (present) , Severe postnatal growth retardation (present) Secondary finding: no
Pathogenic (May 07, 2024)	no assertion criteria provided Method: literature only	ROTHMUND-THOMSON SYNDROME, TYPE 4 Affected status: not provided Allele origin: germline	OMIM Accession: SCV005043130.1 First in ClinVar: May 12, 2024 Last updated: May 12, 2024	Publications: PubMed (1) PubMed: 37055165 Comment on evidence: For discussion of the c.143T-C transition (c.143T-C, NM_001080449.3) in exon 2 of the DNA2 gene, resulting in a leu48-to-pro (L48P) substitution at a highly conserved … (more) For discussion of the c.143T-C transition (c.143T-C, NM_001080449.3) in exon 2 of the DNA2 gene, resulting in a leu48-to-pro (L48P) substitution at a highly conserved residue, that was found in compound heterozygous state in a Brazilian girl (F2) with Rothmund-Thomson syndrome type 4 (RTS4; 620819) by Di Lazzaro Filho et al. (2023), see 601810.0009. (less)

Comment:

Very rare variant, in-silico prediction of damage, in trans with the recurrent splicing variant in 1 proband with classic clinical presentation of Rothmund-Thomson Syndrome with congenital cataracts and severe growth restriction (DNA related RTS).Likely Pathogenic (PM2, PP3, PM3, PP4)

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Biallelic variants in DNA2 cause poikiloderma with congenital cataracts and severe growth failure reminiscent of Rothmund-Thomson syndrome.	Di Lazzaro Filho R	Journal of medical genetics	2023	PMID: 37055165

Text-mined citations for this variant ...

Record last updated Nov 25, 2024

ClinVar Genomic variation as it relates to human health

NM_001080449.3(DNA2):c.143T>C (p.Leu48Pro)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...