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NM_001366145.2(TRPM3):c.4698G>T (p.Arg1566Ser) AND Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skeletal anomalies, with or without seizures

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 19, 2023
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:
RCV004555958.1

Allele description [Variation Report for NM_001366145.2(TRPM3):c.4698G>T (p.Arg1566Ser)]

NM_001366145.2(TRPM3):c.4698G>T (p.Arg1566Ser)

Genes:
KLF9-DT:KLF9 divergent transcript [Gene - HGNC]
TRPM3:transient receptor potential cation channel subfamily M member 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q21.12
Genomic location:
Preferred name:
NM_001366145.2(TRPM3):c.4698G>T (p.Arg1566Ser)
HGVS:
  • NC_000009.12:g.70536415C>A
  • NG_047197.1:g.915510G>T
  • NM_001007471.4:c.4662G>T
  • NM_001366141.2:c.4668G>T
  • NM_001366142.2:c.3997+707G>T
  • NM_001366143.2:c.3961+707G>T
  • NM_001366145.2:c.4698G>TMANE SELECT
  • NM_001366146.2:c.3991+707G>T
  • NM_001366147.2:c.4773G>T
  • NM_001366148.2:c.4036+707G>T
  • NM_001366149.2:c.4668G>T
  • NM_001366150.2:c.3925+707G>T
  • NM_001366151.2:c.3955+707G>T
  • NM_001366152.2:c.4066+707G>T
  • NM_001366154.2:c.3532+707G>T
  • NM_020952.6:c.4203G>T
  • NM_024971.7:c.4239G>T
  • NM_206944.5:c.4173G>T
  • NM_206945.5:c.4209G>T
  • NM_206946.5:c.4278G>T
  • NM_206947.5:c.4248G>T
  • NP_001007472.2:p.Arg1554Ser
  • NP_001353070.1:p.Arg1556Ser
  • NP_001353074.1:p.Arg1566Ser
  • NP_001353076.1:p.Arg1591Ser
  • NP_001353078.1:p.Arg1556Ser
  • NP_066003.3:p.Arg1401Ser
  • NP_079247.5:p.Arg1413Ser
  • NP_996827.3:p.Arg1391Ser
  • NP_996828.3:p.Arg1403Ser
  • NP_996829.3:p.Arg1426Ser
  • NP_996830.3:p.Arg1416Ser
  • NC_000009.11:g.73151331C>A
Protein change:
R1391S
Molecular consequence:
  • NM_001366142.2:c.3997+707G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001366143.2:c.3961+707G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001366146.2:c.3991+707G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001366148.2:c.4036+707G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001366150.2:c.3925+707G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001366151.2:c.3955+707G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001366152.2:c.4066+707G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001366154.2:c.3532+707G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001007471.4:c.4662G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001366141.2:c.4668G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001366145.2:c.4698G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001366147.2:c.4773G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001366149.2:c.4668G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020952.6:c.4203G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024971.7:c.4239G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_206944.5:c.4173G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_206945.5:c.4209G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_206946.5:c.4278G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_206947.5:c.4248G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skeletal anomalies, with or without seizures (NEDFSS)
Identifiers:
MONDO: MONDO:0859365; MedGen: C5830244; OMIM: 620224

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    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV005045039Clinical Genomics Laboratory, Washington University in St. Louis
    criteria provided, single submitter

    (ACMG Guidelines, 2015)    		Uncertain significance
    (Dec 19, 2023)     		germlineclinical testing

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

    Help

    Summary from all submissions

    EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
    not providedgermlineunknownnot providednot 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 Clinical Genomics Laboratory, Washington University in St. Louis, SCV005045039.1

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

    Description

    The TRPM3 c.4698G>T (p.Arg1566Ser) variant, to our knowledge, has not been reported in the medical literature and is absent from the general population (gnomAD v.2.1.1), indicating it is not a common variant. Computational predictors are uncertain as to the impact of this variant on TRPM3 function. Due to limited information, and based on ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), the clinical significance of this variant is uncertain at this time.

    #SampleMethodObservation
    OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
    1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

    Last Updated: May 26, 2024