VCV002445438.4 - ClinVar

NM_005373.3(MPL):c.407C>G (p.Pro136Arg)

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.

(3)

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, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_005373.3(MPL):c.407C>G (p.Pro136Arg)

Variation ID: 2445438 Accession: VCV002445438.4

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 1p34.2 1: 43339286 (GRCh38) [ NCBI UCSC ] 1: 43804957 (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	Jan 25, 2025	Mar 7, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_005373.3:c.407C>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_005364.1:p.Pro136Arg	missense
NC_000001.11:g.43339286C>G
NC_000001.10:g.43804957C>G
NG_007525.1:g.6483C>G
LRG_510:g.6483C>G
LRG_510t1:c.407C>G	LRG_510p1:p.Pro136Arg

... more HGVS ... less HGVS

Protein change

P136R

Other names

Canonical SPDI

NC_000001.11:43339285:C: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

ClinGen: CA339974309 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.
MPL		-	-	GRCh38 GRCh37	774	788

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.
Congenital amegakaryocytic thrombocytopenia	Likely pathogenic (1)	criteria provided, single submitter	-	RCV003154848.2
Congenital amegakaryocytic thrombocytopenia 1	Likely pathogenic (1)	criteria provided, single submitter	Jun 2, 2023	RCV004763608.3
Congenital amegakaryocytic thrombocytopenia 1 Primary myelofibrosis Thrombocythemia 2	Likely pathogenic (1)	criteria provided, single submitter	Mar 7, 2024	RCV005029924.1

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 (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Congenital amegakaryocytic thrombocytopenia 1 Affected status: yes Allele origin: biparental	Dept. of Cytogenetics, ICMR- National Institute of Immunohaematology Accession: SCV003843869.1 First in ClinVar: Mar 26, 2023 Last updated: Mar 26, 2023	Sex: female
Likely pathogenic (Mar 07, 2024)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Primary myelofibrosis Thrombocythemia 2 Congenital amegakaryocytic thrombocytopenia 1 Explanation for multiple conditions: Uncertain. The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases. Affected status: unknown Allele origin: germline	Fulgent Genetics, Fulgent Genetics Accession: SCV005651167.1 First in ClinVar: Jan 25, 2025 Last updated: Jan 25, 2025
Likely pathogenic (Jun 02, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Congenital amegakaryocytic thrombocytopenia 1 (Autosomal recessive inheritance) Affected status: yes Allele origin: germline	Neuberg Centre For Genomic Medicine, NCGM Accession: SCV005373598.3 First in ClinVar: Oct 13, 2024 Last updated: Jan 25, 2025	Comment: The observed missense c.407C>G (p.Pro136Arg) variant in MPL gene has not been reported previously as a pathogenic variant nor as a benign variant, to our … (more) The observed missense c.407C>G (p.Pro136Arg) variant in MPL gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. Another missense variant on the same residue [c.407C>T; p.Pro136Leu] in MPL gene has been reported previously to be disease causing in individuals affected with MPL-related disorders, suggesting that this residue might be of clinical significance (Germeshausen and Ballmaier, 2021). The p.Pro136Arg variant is present with allele frequency of 0.0004% in gnomAD Exomes. This variant has been submitted to the ClinVar database as Likely Pathogenic. The reference amino acid of p.Pro136Arg in MPL is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Pro at position 136 is changed to a Arg changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as a Variant of Uncertain Significance (VUS). (less) Clinical Features: Abnormality of blood and blood-forming tissues (present)

Comment:

The observed missense c.407C>G (p.Pro136Arg) variant in MPL gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. Another missense variant on the same residue [c.407C>T; p.Pro136Leu] in MPL gene has been reported previously to be disease causing in individuals affected with MPL-related disorders, suggesting that this residue might be of clinical significance (Germeshausen and Ballmaier, 2021). The p.Pro136Arg variant is present with allele frequency of 0.0004% in gnomAD Exomes. This variant has been submitted to the ClinVar database as Likely Pathogenic. The reference amino acid of p.Pro136Arg in MPL is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Pro at position 136 is changed to a Arg changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as a Variant of Uncertain Significance (VUS).

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

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Jan 26, 2025

ClinVar Genomic variation as it relates to human health

NM_005373.3(MPL):c.407C>G (p.Pro136Arg)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...