NM_020549.5(CHAT):c.1174G>A (p.Ala392Thr) AND Familial infantile myasthenia

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Jan 29, 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:: RCV000695594.13

Allele description [Variation Report for NM_020549.5(CHAT):c.1174G>A (p.Ala392Thr)]

NM_020549.5(CHAT):c.1174G>A (p.Ala392Thr)

Gene:

CHAT:choline O-acetyltransferase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q11.23

Genomic location:

Preferred name:

NM_020549.5(CHAT):c.1174G>A (p.Ala392Thr)

HGVS:

NC_000010.11:g.49646567G>A
NG_011797.1:g.42473G>A
NM_001142929.2:c.820G>A
NM_001142933.2:c.928G>A
NM_001142934.2:c.820G>A
NM_020549.5:c.1174G>AMANE SELECT
NM_020984.4:c.820G>A
NM_020985.4:c.820G>A
NM_020986.4:c.820G>A
NP_001136401.2:p.Ala274Thr
NP_001136405.2:p.Ala310Thr
NP_001136406.2:p.Ala274Thr
NP_065574.3:p.Ala392Thr
NP_065574.4:p.Ala392Thr
NP_066264.4:p.Ala274Thr
NP_066265.4:p.Ala274Thr
NP_066266.4:p.Ala274Thr
NC_000010.10:g.50854613G>A
NM_020549.4:c.1174G>A

Protein change:

A274T

Links:

dbSNP: rs115877658

NCBI 1000 Genomes Browser:

rs115877658

Molecular consequence:

NM_001142929.2:c.820G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001142933.2:c.928G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001142934.2:c.820G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020549.5:c.1174G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020984.4:c.820G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020985.4:c.820G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020986.4:c.820G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Familial infantile myasthenia (CMS6)
Synonyms:: Congenital myasthenic syndrome with episodic apnea; Myasthenic syndrome congenital associated with episodic apnea; Myasthenic syndrome, presynaptic, congenital, associated with episodic apnea; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009689; MedGen: C0393929; Orphanet: 590; OMIM: 254210

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000824104	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 29, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003833236	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Dec 21, 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

SCV000824104

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 29, 2024)

germline

clinical testing

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

SCV003833236

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Dec 21, 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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000824104.6

#	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 Revvity Omics, Revvity, SCV003833236.2

#	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: Sep 29, 2024

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