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NM_001655.5(ARCN1):c.55C>T (p.Arg19Ter) AND Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Oct 9, 2024
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:
RCV004789814.1

Allele description [Variation Report for NM_001655.5(ARCN1):c.55C>T (p.Arg19Ter)]

NM_001655.5(ARCN1):c.55C>T (p.Arg19Ter)

Gene:
ARCN1:archain 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q23.3
Genomic location:
Preferred name:
NM_001655.5(ARCN1):c.55C>T (p.Arg19Ter)
HGVS:
  • NC_000011.10:g.118581297C>T
  • NG_051953.1:g.13911C>T
  • NM_001142281.2:c.4-1882C>T
  • NM_001425073.1:c.55C>T
  • NM_001425074.1:c.55C>T
  • NM_001425075.1:c.4-6C>T
  • NM_001425076.1:c.-15C>T
  • NM_001425077.1:c.55C>T
  • NM_001425078.1:c.55C>T
  • NM_001425079.1:c.55C>T
  • NM_001425080.1:c.4-2512C>T
  • NM_001425081.1:c.4-1882C>T
  • NM_001655.5:c.55C>TMANE SELECT
  • NP_001412002.1:p.Arg19Ter
  • NP_001412003.1:p.Arg19Ter
  • NP_001412006.1:p.Arg19Ter
  • NP_001412007.1:p.Arg19Ter
  • NP_001412008.1:p.Arg19Ter
  • NP_001646.2:p.Arg19Ter
  • NC_000011.9:g.118452012C>T
  • NM_001655.4:c.55C>T
  • NR_189131.1:n.194C>T
  • NR_189132.1:n.194C>T
Protein change:
R19*
Molecular consequence:
  • NM_001425076.1:c.-15C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001142281.2:c.4-1882C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001425075.1:c.4-6C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001425080.1:c.4-2512C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001425081.1:c.4-1882C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NR_189131.1:n.194C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_189132.1:n.194C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001425073.1:c.55C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001425074.1:c.55C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001425077.1:c.55C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001425078.1:c.55C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001425079.1:c.55C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001655.5:c.55C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay (SSMG)
Synonyms:
SHORT STATURE-MICROGNATHIA SYNDROME
Identifiers:
MONDO: MONDO:0014948; MedGen: C4310686; OMIM: 617164

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005400516Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Oct 9, 2024) 		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, SCV005400516.1

#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 Likely Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with short stature-micrognathia syndrome (MIM#617164). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0204 - Variant is predicted to result in a truncated protein (premature termination codon is located within the first 102 nucleotides of the coding sequence and is predicted to escape nonsense-mediated decay). (SP) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0704 - Another 5' truncating variant comparable to the one identified in this case has limited previous evidence for pathogenicity. p.(Arg26*) has been classified as a pathogenic variant in ClinVar; however, no phenotypic information was provided. (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) 1203 - This variant has been shown to be de novo in the proband (parental status confirmed) (by trio analysis). (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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

Last Updated: Nov 30, 2024