NM_001243177.4(ALDOA):c.1201G>A (p.Gly401Ser) AND HNSHA due to aldolase A deficiency

Germline classification:: Conflicting interpretations of pathogenicity (5 submissions)
Last evaluated:: Jan 31, 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:: RCV000314539.25

Allele description [Variation Report for NM_001243177.4(ALDOA):c.1201G>A (p.Gly401Ser)]

NM_001243177.4(ALDOA):c.1201G>A (p.Gly401Ser)

Genes:

ALDOA:aldolase, fructose-bisphosphate A [Gene - OMIM - HGNC]
LOC112694756:uncharaterized LOC112694756 [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

16p11.2

Genomic location:

Preferred name:

NM_001243177.4(ALDOA):c.1201G>A (p.Gly401Ser)

Other names:

NM_000034.3:c.1039G>A

HGVS:

NC_000016.10:g.30070156G>A
NG_008010.1:g.21987G>A
NM_001127617.2:c.1039G>A
NM_001243177.4:c.1201G>AMANE SELECT
NM_001365304.2:c.*1548G>AMANE SELECT
NM_001365305.2:c.*1548G>A
NM_001365307.2:c.*1548G>A
NM_184041.5:c.1039G>A
NM_184043.2:c.1039G>A
NP_001121089.1:p.Gly347Ser
NP_001230106.1:p.Gly401Ser
NP_908930.1:p.Gly347Ser
NP_908932.1:p.Gly347Ser
LRG_1180t1:c.1039G>A
LRG_1180t2:c.1201G>A
LRG_1180:g.21987G>A
LRG_1180p1:p.Gly347Ser
LRG_1180p2:p.Gly401Ser
NC_000016.9:g.30081477G>A
P04075:p.Gly347Ser

Protein change:

G347S

Links:

UniProtKB: P04075#VAR_044144; dbSNP: rs138824667

NCBI 1000 Genomes Browser:

rs138824667

Molecular consequence:

NM_001365304.2:c.*1548G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001365305.2:c.*1548G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001365307.2:c.*1548G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001127617.2:c.1039G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001243177.4:c.1201G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_184041.5:c.1039G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_184043.2:c.1039G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: HNSHA due to aldolase A deficiency (GSD12)
Synonyms:: GLYCOGEN STORAGE DISEASE XII; GSD XII; Glycogen storage disease type 12; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0012747; MedGen: C0272066; Orphanet: 57; OMIM: 611881

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000396460	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification 20161018)	Uncertain significance (Jun 14, 2016)	germline	clinical testing	ICSL_Variant_Classification_20161018.pdf, Citation Link,
SCV001140087	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Likely benign (May 28, 2019)	unknown	clinical testing	Citation Link,
SCV001732401	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 31, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002075086	GenomeConnect, ClinGen	no classification provided	not provided	maternal	phenotyping only
SCV003799740	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2021)	Likely benign (Mar 22, 2022)	germline	clinical testing	Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	maternal	unknown	not provided	not provided	not provided	not provided	not provided	phenotyping only
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000396460.2

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

From Mendelics, SCV001140087.1

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

From Invitae, SCV001732401.4

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

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

From GenomeConnect, ClinGen, SCV002075086.1

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

Description

Variant interpreted as Uncertain significance and reported on 10-14-2017 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV003799740.2

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

Last Updated: May 19, 2024

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