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NM_058172.6(ANTXR2):c.1074del (p.Ala359fs)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Feb 21, 2021)
Last evaluated:
Nov 14, 2019
Accession:
VCV000419342.5
Variation ID:
419342
Description:
1bp deletion
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NM_058172.6(ANTXR2):c.1074del (p.Ala359fs)

Allele ID
406466
Variant type
Deletion
Variant length
1 bp
Cytogenetic location
4q21.21
Genomic location
4: 79984831 (GRCh38) GRCh38 UCSC
4: 80905985 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000004.11:g.80905985del
NC_000004.12:g.79984831del
NG_015987.1:g.93493del
... more HGVS
Protein change
A282fs, A359fs
Other names
-
Canonical SPDI
NC_000004.12:79984830:A:
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00002
The Genome Aggregation Database (gnomAD) 0.00003
The Genome Aggregation Database (gnomAD), exomes 0.00004
Links
ClinGen: CA2981725
dbSNP: rs312262693
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 3 criteria provided, multiple submitters, no conflicts Nov 14, 2019 RCV001261562.3
Pathogenic 1 criteria provided, single submitter Feb 15, 2018 RCV000483857.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ANTXR2 - - GRCh38
GRCh37
215 242

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Feb 15, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000567074.3
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The c.1074delT deletion in the ANTXR2 gene is one of three frameshift variants in the exon 13 hotspotthat accounts for approximately 60% of all pathogenic … (more)
Pathogenic
(-)
criteria provided, single submitter
Method: clinical testing
Hyaline fibromatosis syndrome
Allele origin: germline
Pathology and Clinical Laboratory Medicine,King Fahad Medical City
Accession: SCV001438828.1
Submitted: (May 26, 2020)
Evidence details
Pathogenic
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
HYALINE FIBROMATOSIS SYNDROME
Allele origin: germline
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego
Accession: SCV001445921.1
Submitted: (Jul 31, 2020)
Evidence details
Comment:
This frameshifting variant in exon 13 of 16 introduces a premature stop codon and is therefore predicted to result in loss of normal protein function. … (more)
Pathogenic
(Nov 14, 2019)
criteria provided, single submitter
Method: clinical testing
Hyaline fibromatosis syndrome
Allele origin: unknown
Baylor Genetics
Accession: SCV001523657.1
Submitted: (Feb 21, 2021)
Evidence details
Comment:
This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs312262693...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 08, 2021