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NM_001382241.1(TNPO2):c.1643C>T (p.Ser548Phe) AND Intellectual developmental disorder with hypotonia, impaired speech, and dysmorphic facies

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Feb 3, 2022
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:
RCV002253064.2

Allele description [Variation Report for NM_001382241.1(TNPO2):c.1643C>T (p.Ser548Phe)]

NM_001382241.1(TNPO2):c.1643C>T (p.Ser548Phe)

Gene:
TNPO2:transportin 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.13
Genomic location:
Preferred name:
NM_001382241.1(TNPO2):c.1643C>T (p.Ser548Phe)
Other names:
p.Ser548Phe
HGVS:
  • NC_000019.10:g.12706221G>A
  • NM_001136195.2:c.1643C>T
  • NM_001136196.2:c.1643C>T
  • NM_001382236.1:c.1643C>T
  • NM_001382237.1:c.1643C>T
  • NM_001382238.1:c.1643C>T
  • NM_001382239.1:c.1643C>T
  • NM_001382240.1:c.1643C>T
  • NM_001382241.1:c.1643C>TMANE SELECT
  • NM_001382242.1:c.1643C>T
  • NM_001382243.1:c.1643C>T
  • NM_013433.5:c.1643C>T
  • NP_001129667.1:p.Ser548Phe
  • NP_001129668.1:p.Ser548Phe
  • NP_001369165.1:p.Ser548Phe
  • NP_001369166.1:p.Ser548Phe
  • NP_001369167.1:p.Ser548Phe
  • NP_001369168.1:p.Ser548Phe
  • NP_001369169.1:p.Ser548Phe
  • NP_001369170.1:p.Ser548Phe
  • NP_001369171.1:p.Ser548Phe
  • NP_001369172.1:p.Ser548Phe
  • NP_038461.2:p.Ser548Phe
  • NC_000019.9:g.12817035G>A
  • NM_001136196.1:c.1643C>T
  • NR_167974.1:n.1782C>T
  • NR_167975.1:n.1937C>T
  • NR_167976.1:n.1908C>T
  • NR_167977.1:n.1908C>T
  • NR_167978.1:n.1513C>T
  • NR_167979.1:n.1753C>T
Protein change:
S548F
Links:
dbSNP: rs2145492753
NCBI 1000 Genomes Browser:
rs2145492753
Molecular consequence:
  • NM_001136195.2:c.1643C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136196.2:c.1643C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382236.1:c.1643C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382237.1:c.1643C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382238.1:c.1643C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382239.1:c.1643C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382240.1:c.1643C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382241.1:c.1643C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382242.1:c.1643C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382243.1:c.1643C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_013433.5:c.1643C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_167974.1:n.1782C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_167975.1:n.1937C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_167976.1:n.1908C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_167977.1:n.1908C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_167978.1:n.1513C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_167979.1:n.1753C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Name:
Intellectual developmental disorder with hypotonia, impaired speech, and dysmorphic facies (IDDHISD)
Identifiers:
MONDO: MONDO:0859197; MedGen: C5561997; OMIM: 619556

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002523178Undiagnosed Diseases Network, NIH - Undiagnosed Diseases Network (NIH), UDN
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Feb 3, 2022) 		de novoclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedde novoyes11not 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 Undiagnosed Diseases Network, NIH - Undiagnosed Diseases Network (NIH), UDN, SCV002523178.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

This variant has been previously published in a different individual (PMID: 34314705).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot provided1not provided1not provided

Last Updated: Dec 24, 2023