NM_001134363.3(RBM20):c.2116C>A (p.Pro706Thr) AND Dilated cardiomyopathy 1DD

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Jan 14, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV000685352.14

Allele description [Variation Report for NM_001134363.3(RBM20):c.2116C>A (p.Pro706Thr)]

NM_001134363.3(RBM20):c.2116C>A (p.Pro706Thr)

Gene:

RBM20:RNA binding motif protein 20 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q25.2

Genomic location:

Preferred name:

NM_001134363.3(RBM20):c.2116C>A (p.Pro706Thr)

Other names:

p.P706T:CCC>ACC

HGVS:

NC_000010.11:g.110812513C>A
NG_021177.1:g.173117C>A
NM_001134363.3:c.2116C>AMANE SELECT
NP_001127835.2:p.Pro706Thr
LRG_382t1:c.2116C>A
LRG_382:g.173117C>A
NC_000010.10:g.112572271C>A
NM_001134363.1:c.2116C>A
NM_001134363.2:c.2116C>A

Protein change:

P706T

Links:

dbSNP: rs373797219

NCBI 1000 Genomes Browser:

rs373797219

Molecular consequence:

NM_001134363.3:c.2116C>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Dilated cardiomyopathy 1DD (CMD1DD)
Identifiers:: MONDO: MONDO:0013168; MedGen: C2750995; Orphanet: 154; OMIM: 613172

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000812830	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 14, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002557058	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Feb 2, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 29892087, 25741868
SCV004805227	Clinical Genomics Laboratory, Stanford Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jun 7, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000812830

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 14, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002557058

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Feb 2, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV004805227

Clinical Genomics Laboratory, Stanford Medicine

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jun 7, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

A gene-centric strategy for identifying disease-causing rare variants in dilated cardiomyopathy.

Horvat C, Johnson R, Lam L, Munro J, Mazzarotto F, Roberts AM, Herman DS, Parfenov M, Haghighi A, McDonough B, DePalma SR, Keogh AM, Macdonald PS, Hayward CS, Roberts A, Barton PJR, Felkin LE, Giannoulatou E, Cook SA, Seidman JG, Seidman CE, Fatkin D.

Genet Med. 2019 Jan;21(1):133-143. doi: 10.1038/s41436-018-0036-2. Epub 2018 Jun 11.

PubMed [citation]

PMID:: 29892087
PMCID:: PMC7336363

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000812830.7

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

#	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

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002557058.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3C. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with dilated cardiomyopathy, 1DD (MIM#613172) (OMIM). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from proline to threonine. (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (13 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v3) (1 heterozygote, 0 homozygotes). (I) 0503 - Missense variant consistently predicted to be tolerated by multiple in silico tools or not conserved in placental mammals with a minor amino acid change. (SB) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0808 - Previous reports of pathogenicity for this variant are conflicting. This variant has been reported in a family with DCM, although this variant was shown not to segregate with disease in this family (PMID: 29892087). This variant has also been reported as a VUS and likely benign in ClinVar and Global Variome shared LOVD. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

#	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

From Clinical Genomics Laboratory, Stanford Medicine, SCV004805227.1

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

Description

The p.Pro706Thr variant in the RBM20 gene has not been previously reported in association with disease. This variant has been identified in 13/186,024 chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org/). Although this variant has been seen in the general population, it has not been observed at a frequency high enough to rule out pathogenicity. The proline at position 706 is not evolutionarily conserved and several mammalian species have a threonine at this position. Computational tools predict that the p.Pro706Thr does not impact protein function; however, the accuracy of in silico algorithms is limited. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, the significance of the p.Pro706Thr variant is uncertain. Additional information is needed to resolve the significance of this variant. [ACMG evidence codes used: BP4]

#	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		1	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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