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NM_006097.5(MYL9):c.184+2_184+10del AND Visceral myopathy 1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 26, 2020
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:
RCV001009609.2

Allele description [Variation Report for NM_006097.5(MYL9):c.184+2_184+10del]

NM_006097.5(MYL9):c.184+2_184+10del

Genes:
DLGAP4-AS1:DLGAP4 antisense RNA 1 [Gene - HGNC]
MYL9:myosin light chain 9 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
20q11.23
Genomic location:
Preferred name:
NM_006097.5(MYL9):c.184+2_184+10del
HGVS:
  • NC_000020.11:g.36545070_36545078del
  • NM_006097.5:c.184+2_184+10delMANE SELECT
  • NM_181526.3:c.184+2_184+10del
  • NC_000020.10:g.35173473_35173481del
  • NM_006097.4:c.184+2_184+10del
  • NM_181526.2:c.184+2_184+10del
Links:
OMIM: 609905.0001; dbSNP: rs1569529545
NCBI 1000 Genomes Browser:
rs1569529545
Molecular consequence:
  • NM_006097.5:c.184+2_184+10del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_181526.3:c.184+2_184+10del - splice donor variant - [Sequence Ontology: SO:0001575]
Observations:
1

Condition(s)

Name:
Visceral myopathy 1 (VSCM1)
Synonyms:
Megaduodenum and/or megacystis; Pseudoobstruction idiopathic intestinal; Visceral myopathy; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0020754; MedGen: C5542197; Orphanet: 2604; OMIM: 155310

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001164303Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Feb 26, 2020) 		paternalclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedpaternalyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Fulgent Genetics, Fulgent Genetics, SCV001164303.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (1)

Description

Seen in trans with exon 4 deletion in MYL9

Description

This intronic variant, NM_006097.4:c.184+2_184+10del, was identified in trans with a heterozygous deletion of exon 4 in an individual with a clinical diagnosis of MMIH syndrome: bilateral hydronephrosis, megacystis, congenital bilateral mydriasis, lack of urinary bladder peristalsis, and intestinal pseudo-obstruction. This intronic variant alters the highly conserved splice donor site for exon 2 of this transcript and is predicted by five splice site prediction tools queried to abolish canonical splice donor activity. This variant is expected to result in altered function of the MYL9 gene product as a result of aberrant splicing. This variant has been observed at a frequency of less than 0.01% (2/245706 alleles) across the entire Broad data set (individuals without severe childhood onset disease).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1paternalyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Aug 5, 2023