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NM_002180.3(IGHMBP2):c.1693G>A (p.Asp565Asn)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jul 4, 2021)
Last evaluated:
Mar 6, 2020
Accession:
VCV000581680.13
Variation ID:
581680
Description:
single nucleotide variant
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NM_002180.3(IGHMBP2):c.1693G>A (p.Asp565Asn)

Allele ID
564895
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q13.3
Genomic location
11: 68935359 (GRCh38) GRCh38 UCSC
11: 68702827 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.68935359G>A
NG_007976.1:g.36509G>A
NM_002180.3:c.1693G>A MANE Select NP_002171.2:p.Asp565Asn missense
... more HGVS
Protein change
D565N
Other names
-
Canonical SPDI
NC_000011.10:68935358:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00002
The Genome Aggregation Database (gnomAD) 0.00003
Exome Aggregation Consortium (ExAC) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Links
dbSNP: rs770111639
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Mar 6, 2020 RCV000705582.4
Pathogenic 1 criteria provided, single submitter Oct 1, 2019 RCV001090413.2
Likely pathogenic 1 no assertion criteria provided - RCV000768429.2
Uncertain significance 1 no assertion criteria provided - RCV000790283.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
IGHMBP2 - - GRCh38
GRCh37
822 838

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Mar 06, 2020)
criteria provided, single submitter
Method: clinical testing
Spinal muscular atrophy, distal, autosomal recessive, 1
Charcot-Marie-Tooth disease, axonal, type 2S
Allele origin: germline
Invitae
Accession: SCV000834584.4
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (5)
Comment:
This sequence change replaces aspartic acid with asparagine at codon 565 of the IGHMBP2 protein (p.Asp565Asn). The aspartic acid residue is highly conserved and there … (more)
Pathogenic
(Oct 01, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001245955.6
Submitted: (Jul 04, 2021)
Evidence details
Likely pathogenic
(-)
no assertion criteria provided
Method: case-control
Charcot-Marie-Tooth disease, axonal, type 2S
Allele origin: inherited
Biochemistry Laboratory of CDMU,Chengde Medical University
Accession: SCV000899184.1
Submitted: (Apr 15, 2019)
Evidence details
Uncertain significance
(-)
no assertion criteria provided
Method: literature only
Distal spinal muscular atrophy
Allele origin: germline
Inherited Neuropathy Consortium
Accession: SCV000929687.1
Submitted: (Jul 10, 2019)
Evidence details
Publications
PubMed (1)

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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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
The natural course of infantile spinal muscular atrophy with respiratory distress type 1 (SMARD1). Eckart M Pediatrics 2012 PMID: 22157136
IGHMBP2 is a ribosome-associated helicase inactive in the neuromuscular disorder distal SMA type 1 (DSMA1). Guenther UP Human molecular genetics 2009 PMID: 19158098
Allelic heterogeneity of SMARD1 at the IGHMBP2 locus. Maystadt I Human mutation 2004 PMID: 15108294
Infantile spinal muscular atrophy with respiratory distress type 1 (SMARD1). Grohmann K Annals of neurology 2003 PMID: 14681881

Text-mined citations for rs770111639...

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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 30, 2021