NM_005566.4(LDHA):c.999_*1del (p.Phe332_Ter333insTer) AND Glycogen storage disease due to lactate dehydrogenase M-subunit deficiency

Germline classification:: Likely benign (1 submission)
Last evaluated:: Aug 19, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003075772.3

Allele description [Variation Report for NM_005566.4(LDHA):c.999_*1del (p.Phe332_Ter333insTer)]

NM_005566.4(LDHA):c.999_*1del (p.Phe332_Ter333insTer)

Gene:

LDHA:lactate dehydrogenase A [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11p15.1

Genomic location:

Preferred name:

NM_005566.4(LDHA):c.999_*1del (p.Phe332_Ter333insTer)

HGVS:

NC_000011.10:g.18407281_18407282del
NG_008185.1:g.17847_17848del
NM_001135239.2:c.825_*1del
NM_001165414.2:c.1086_*1del
NM_001165415.2:c.730_731del
NM_001165416.2:c.*149_*150del
NM_005566.4:c.999_*1delMANE SELECT
NP_001128711.1:p.Phe274_Ter275insTer
NP_001158886.1:p.Phe361_Ter362insTer
NP_001158887.1:p.Lys244fs
NP_005557.1:p.Phe332_Ter333insTer
NC_000011.9:g.18428827_18428828del
NC_000011.9:g.18428828_18428829del
NR_028500.2:n.979_980del

Protein change:

K244fs

Molecular consequence:

NM_001165416.2:c.*149_*150del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001135239.2:c.825_*1del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001165414.2:c.1086_*1del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001165415.2:c.730_731del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_005566.4:c.999_*1del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_028500.2:n.979_980del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
Synonyms:: GSD XI; LACTATE DEHYDROGENASE A DEFICIENCY; Glycogen storage disease XI
Identifiers:: MONDO: MONDO:0013047; MedGen: C2931743; Orphanet: 284426; OMIM: 612933

Recent activity

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Homo sapiens LIM zinc finger domain containing 2 (LIMS2), transcript variant 3, ...
Homo sapiens LIM zinc finger domain containing 2 (LIMS2), transcript variant 3, mRNA
gi|1813795618|ref|NM_001161403.3|

Nucleotide
Homo sapiens LIM and senescent cell antigen-like domains 2, mRNA (cDNA clone MGC...
Homo sapiens LIM and senescent cell antigen-like domains 2, mRNA (cDNA clone MGC:75000 IMAGE:6181259), complete cds
gi|41350928|gb|BC065816.1|

Nucleotide
zinc finger protein 593 [Cucurbita moschata]
zinc finger protein 593 [Cucurbita moschata]
gi|1279817909|ref|XP_022962632.1|

Protein
protein CNGC15b-like [Cucurbita moschata]
protein CNGC15b-like [Cucurbita moschata]
gi|1279830806|ref|XP_022925648.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003472319	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Aug 19, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003472319

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Aug 19, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003472319.2

#	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

Last Updated: Oct 8, 2024

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