NM_002087.4(GRN):c.26C>A (p.Ala9Asp) AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Aug 1, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000084421.23

Allele description [Variation Report for NM_002087.4(GRN):c.26C>A (p.Ala9Asp)]

NM_002087.4(GRN):c.26C>A (p.Ala9Asp)

Gene:

GRN:granulin precursor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q21.31

Genomic location:

Preferred name:

NM_002087.4(GRN):c.26C>A (p.Ala9Asp)

HGVS:

NC_000017.11:g.44349190C>A
NG_007886.1:g.9068C>A
NM_002087.4:c.26C>AMANE SELECT
NP_002078.1:p.Ala9Asp
LRG_661t1:c.26C>A
LRG_661:g.9068C>A
NC_000017.10:g.42426558C>A
NM_002087.2:c.26C>A
P28799:p.Ala9Asp

Protein change:

A9D; ALA9ASP

Links:

UniProtKB: P28799#VAR_044451; OMIM: 138945.0008; dbSNP: rs63751243

NCBI 1000 Genomes Browser:

rs63751243

Molecular consequence:

NM_002087.4:c.26C>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000116557	VIB Department of Molecular Genetics, University of Antwerp	no classification provided	not provided	unknown	not provided
SCV001475244	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Pathogenic (Mar 20, 2020)	unknown	clinical testing	PubMed (11) [See all records that cite these PMIDs] 17917583, 16950801, 16983685, 17984093, 18183624, 18322394, 21482928, 23596077, 29874572, 31262553, 26467025
SCV001961697	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Aug 1, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000116557

VIB Department of Molecular Genetics, University of Antwerp

no classification provided

not provided

unknown

not provided

SCV001475244

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Pathogenic
(Mar 20, 2020)

unknown

clinical testing

PubMed (11)
[See all records that cite these PMIDs]

SCV001961697

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Aug 1, 2021)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	not provided	not provided	not provided	not provided	not provided	1	not provided	literature only
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Corticobasal syndrome associated with the A9D Progranulin mutation.

Spina S, Murrell JR, Huey ED, Wassermann EM, Pietrini P, Grafman J, Ghetti B.

J Neuropathol Exp Neurol. 2007 Oct;66(10):892-900.

PubMed [citation]

PMID:: 17917583

Mutations in progranulin are a major cause of ubiquitin-positive frontotemporal lobar degeneration.

Gass J, Cannon A, Mackenzie IR, Boeve B, Baker M, Adamson J, Crook R, Melquist S, Kuntz K, Petersen R, Josephs K, Pickering-Brown SM, Graff-Radford N, Uitti R, Dickson D, Wszolek Z, Gonzalez J, Beach TG, Bigio E, Johnson N, Weintraub S, Mesulam M, et al.

Hum Mol Genet. 2006 Oct 15;15(20):2988-3001. Epub 2006 Sep 1.

PubMed [citation]

PMID:: 16950801

See all PubMed Citations (11)

Details of each submission

From VIB Department of Molecular Genetics, University of Antwerp, SCV000116557.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	not provided	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	not provided	1	not provided	not provided		not provided	not provided	not provided	not provided

From Athena Diagnostics, SCV001475244.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (11)

Description

Not found in the total gnomAD dataset, and the data is high quality. Predicted to have a damaging effect on the protein. Found in multiple individuals with expected phenotype for this gene. Assessment of experimental evidence suggests this variant results in abnormal protein function.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV001961697.20

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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