VCV002683804.1 - ClinVar

NM_020647.4(JPH1):c.1738del (p.Leu580fs)

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_020647.4(JPH1):c.1738del (p.Leu580fs)

Variation ID: 2683804 Accession: VCV002683804.1

Type and length

Deletion, 1 bp

Location

Cytogenetic: 8q21.11 8: 74244696 (GRCh38) [ NCBI UCSC ] 8: 75156931 (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	Jul 15, 2024	Oct 8, 2024	Nov 17, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_020647.4:c.1738del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_065698.1:p.Leu580fs	frameshift
NM_001317830.2:c.1738del	NP_001304759.1:p.Leu580fs	frameshift
NM_001363050.1:c.1738del	NP_001349979.1:p.Leu580fs	frameshift
NM_001363051.1:c.1738del	NP_001349980.1:p.Leu580fs	frameshift
NC_000008.11:g.74244696del
NC_000008.10:g.75156931del
NG_046331.1:g.81632del

... more HGVS ... less HGVS

Protein change

L580fs

Other names

Canonical SPDI

NC_000008.11:74244695: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: 605266.0004 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.
JPH1		-	-	GRCh38 GRCh37	45	78

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 MYOPATHY 25	Pathogenic (1)	no assertion criteria provided	Sep 26, 2024	RCV004780563.1
Congenital myopathy	Likely pathogenic (1)	criteria provided, single submitter	Nov 17, 2023	RCV004585043.1

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 (Nov 17, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: research	Congenital Myopathy Affected status: yes Allele origin: germline	Harry Perkins Institute Of Medical Research, University Of Western Australia Accession: SCV004228296.1 First in ClinVar: Jul 15, 2024 Last updated: Jul 15, 2024	Sex: female
Pathogenic (Sep 26, 2024)	no assertion criteria provided Method: literature only	CONGENITAL MYOPATHY 25 Affected status: not provided Allele origin: germline	OMIM Accession: SCV005328504.1 First in ClinVar: Oct 08, 2024 Last updated: Oct 08, 2024	Publications: PubMed (1) PubMed: 39209426 Comment on evidence: In a patient (F3-II.1), born to consanguineous parents, with congenital myopathy-25 (CMYO25; 620964), Johari et al. (2024) identified homozygosity for a 1-bp deletion (c.1738delC) in … (more) In a patient (F3-II.1), born to consanguineous parents, with congenital myopathy-25 (CMYO25; 620964), Johari et al. (2024) identified homozygosity for a 1-bp deletion (c.1738delC) in the JPH1 gene, predicted to result in a frameshift and premature termination (Leu580TrpfsTer16). The mutation, which was found by whole-genome sequencing, was present in heterozygous state in the parents. JPH1 expression was reduced in patient muscle tissue compared to controls. (less)

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.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Loss-of-function variants in JPH1 cause congenital myopathy with prominent facial and ocular involvement.	Johari M	Journal of medical genetics	2024	PMID: 39209426

Text-mined citations for this variant ...

Record last updated Nov 10, 2024

ClinVar Genomic variation as it relates to human health

NM_020647.4(JPH1):c.1738del (p.Leu580fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...