NM_058172.6(ANTXR2):c.134T>C (p.Leu45Pro) AND Hyaline fibromatosis syndrome

Clinical significance:Pathogenic (Last evaluated: Jun 3, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV001261563.3

Allele description [Variation Report for NM_058172.6(ANTXR2):c.134T>C (p.Leu45Pro)]

NM_058172.6(ANTXR2):c.134T>C (p.Leu45Pro)

Gene:
ANTXR2:ANTXR cell adhesion molecule 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
4q21.21
Genomic location:
Preferred name:
NM_058172.6(ANTXR2):c.134T>C (p.Leu45Pro)
HGVS:
  • NC_000004.12:g.80072427A>G
  • NG_015987.1:g.5897T>C
  • NM_001145794.1:c.134T>C
  • NM_001145794.2:c.134T>C
  • NM_001286780.2:c.-79-773T>C
  • NM_001286781.2:c.-80+282T>C
  • NM_058172.6:c.134T>CMANE SELECT
  • NP_001139266.1:p.Leu45Pro
  • NP_001139266.1:p.Leu45Pro
  • NP_477520.2:p.Leu45Pro
  • NC_000004.11:g.80993581A>G
  • NM_058172.5:c.134T>C
  • P58335:p.Leu45Pro
Protein change:
L45P
Links:
UniProtKB: P58335#VAR_022687; dbSNP: rs886041401
NCBI 1000 Genomes Browser:
rs886041401
Molecular consequence:
  • NM_001286780.2:c.-79-773T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001286781.2:c.-80+282T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001145794.1:c.134T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001145794.2:c.134T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_058172.6:c.134T>C - missense variant - [Sequence Ontology: SO:0001583]
Observations:
2

Condition(s)

Name:
Hyaline fibromatosis syndrome (HFS)
Synonyms:
HYALINOSIS, SYSTEMIC; Hyalinosis, Inherited Systemic
Identifiers:
MONDO: MONDO:0009229; MedGen: C2745948; Orphanet: 2028; OMIM: 228600

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001438829Pathology and Clinical Laboratory Medicine,King Fahad Medical Citycriteria provided, single submitter
Pathogenicgermlineclinical testing

Citation Link,

SCV001469151Biochemical Molecular Genetic Laboratory,King Abdulaziz Medical Cityno assertion criteria providedLikely pathogenic
(Nov 12, 2020)
germlineclinical testing

SCV001523658Baylor Geneticscriteria provided, single submitter
Pathogenic
(Jun 3, 2020)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
Arabgermlineyes2not 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 Pathology and Clinical Laboratory Medicine,King Fahad Medical City, SCV001438829.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Arab2not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided

From Biochemical Molecular Genetic Laboratory,King Abdulaziz Medical City, SCV001469151.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV001523658.1

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

Description

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

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

Last Updated: Oct 24, 2021

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