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NM_020971.3(SPTBN4):c.5173C>T (p.Gln1725Ter) AND Neurodevelopmental disorder with hypotonia, neuropathy, and deafness

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 17, 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:
RCV004595099.1

Allele description [Variation Report for NM_020971.3(SPTBN4):c.5173C>T (p.Gln1725Ter)]

NM_020971.3(SPTBN4):c.5173C>T (p.Gln1725Ter)

Gene:
SPTBN4:spectrin beta, non-erythrocytic 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19q13.2
Genomic location:
Preferred name:
NM_020971.3(SPTBN4):c.5173C>T (p.Gln1725Ter)
HGVS:
  • NC_000019.10:g.40556172C>T
  • NG_029905.1:g.93953C>T
  • NG_029905.2:g.94173C>T
  • NM_020971.3:c.5173C>TMANE SELECT
  • NM_025213.3:c.1201C>T
  • NP_066022.2:p.Gln1725Ter
  • NP_079489.2:p.Gln401Ter
  • NC_000019.9:g.41062078C>T
  • NM_020971.2:c.5173C>T
Protein change:
Q1725*
Molecular consequence:
  • NM_020971.3:c.5173C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_025213.3:c.1201C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Neurodevelopmental disorder with hypotonia, neuropathy, and deafness (NEDHND)
Synonyms:
Myopathy, congenital, with neuropathy and deafness
Identifiers:
MONDO: MONDO:0060496; MedGen: C4479603; OMIM: 617519

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005087184Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Jul 17, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot 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 Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV005087184.1

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

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with neurodevelopmental disorder with hypotonia, neuropathy, and deafness (MIM#617519). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0701 - Other NMD predicted variants comparable to the one identified in this case have very strong previous evidence for pathogenicity (DECIPHER). (SP) 0807 - This variant has no previous evidence of pathogenicity. (I) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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

Last Updated: Aug 4, 2024