NM_213720.3(CHCHD10):c.313G>A (p.Glu105Lys) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 25, 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:: RCV002903277.2

Allele description [Variation Report for NM_213720.3(CHCHD10):c.313G>A (p.Glu105Lys)]

NM_213720.3(CHCHD10):c.313G>A (p.Glu105Lys)

Gene:

CHCHD10:coiled-coil-helix-coiled-coil-helix domain containing 10 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q11.23

Genomic location:

Preferred name:

NM_213720.3(CHCHD10):c.313G>A (p.Glu105Lys)

HGVS:

NC_000022.11:g.23766224C>T
NG_034223.1:g.6749G>A
NG_145141.1:g.815C>T
NG_145142.1:g.15C>T
NM_001301339.2:c.334G>A
NM_213720.3:c.313G>AMANE SELECT
NP_001288268.1:p.Glu112Lys
NP_998885.1:p.Glu105Lys
NC_000022.10:g.24108411C>T
NR_125755.2:n.358G>A
NR_125756.2:n.191G>A

Protein change:

E105K

Molecular consequence:

NM_001301339.2:c.334G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_213720.3:c.313G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_125755.2:n.358G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_125756.2:n.191G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Lower motor neuron syndrome with late-adult onset (SMAJ)
Synonyms:: Spinal muscular atrophy, Jokela type
Identifiers:: MONDO: MONDO:0014025; MedGen: C3554398; Orphanet: 276435; OMIM: 615048

Name:: Frontotemporal dementia and/or amyotrophic lateral sclerosis 2
Synonyms:: FTDALS2
Identifiers:: MONDO: MONDO:0014395; MedGen: C4014648; Orphanet: 275872; OMIM: 615911

Name:: Autosomal dominant mitochondrial myopathy with exercise intolerance (IMMD)
Synonyms:: Myopathy, isolated mitochondrial, autosomal dominant
Identifiers:: MONDO: MONDO:0014532; MedGen: C4015513; Orphanet: 457050; OMIM: 616209

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Homo sapiens DNA polymerase delta 1, catalytic subunit (POLD1), transcript varia...
Homo sapiens DNA polymerase delta 1, catalytic subunit (POLD1), transcript variant 3, non-coding RNA
gi|1700660572|ref|NR_046402.2|

Nucleotide
RecName: Full=Retrotransposon Gag-like protein 8C; AltName: Full=Mammalian retro...
RecName: Full=Retrotransposon Gag-like protein 8C; AltName: Full=Mammalian retrotransposon derived protein 8C
gi|160385728|sp|A6ZKI3.1|RTL8C_HUMA

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003248258	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 25, 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

SCV003248258

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 25, 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 Invitae, SCV003248258.2

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

Description

Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals affected with CHCHD10-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.01%). This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 105 of the CHCHD10 protein (p.Glu105Lys).

#	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: Feb 28, 2024

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