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NM_001379500.1(COL18A1):c.1248G>A (p.Pro416=) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Jan 2, 2024
Review status:
criteria provided, conflicting classifications
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:
RCV001898439.10

Allele description [Variation Report for NM_001379500.1(COL18A1):c.1248G>A (p.Pro416=)]

NM_001379500.1(COL18A1):c.1248G>A (p.Pro416=)

Gene:
COL18A1:collagen type XVIII alpha 1 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
21q22.3
Genomic location:
Preferred name:
NM_001379500.1(COL18A1):c.1248G>A (p.Pro416=)
Other names:
NM_130445.2:c.1248G>A
HGVS:
  • NC_000021.9:g.45478353G>A
  • NG_011903.1:g.78171G>A
  • NM_001379500.1:c.1248G>AMANE SELECT
  • NM_030582.4:c.1788G>A
  • NM_130444.3:c.2493G>A
  • NP_001366429.1:p.Pro416=
  • NP_085059.2:p.Pro596=
  • NP_569711.2:p.Pro831=
  • NC_000021.8:g.46898267G>A
Links:
dbSNP: rs185296216
NCBI 1000 Genomes Browser:
rs185296216
Molecular consequence:
  • NM_001379500.1:c.1248G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_030582.4:c.1788G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_130444.3:c.2493G>A - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002159638Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Jan 2, 2024)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV004146722CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Likely benign
(Apr 1, 2022)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]
PMID:
17576681
PMCID:
PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]
PMID:
9536098
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002159638.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change affects codon 416 of the COL18A1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the COL18A1 protein. This variant also falls at the last nucleotide of exon 9, which is part of the consensus splice site for this exon. This variant is present in population databases (rs185296216, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with COL18A1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1394102). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

From CeGaT Center for Human Genetics Tuebingen, SCV004146722.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

COL18A1: BP4, BP7

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jun 17, 2024