NM_015166.4(MLC1):c.626C>A (p.Ala209Asp) AND Megalencephalic leukoencephalopathy with subcortical cysts 1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 1, 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:: RCV002283818.1

Allele description [Variation Report for NM_015166.4(MLC1):c.626C>A (p.Ala209Asp)]

NM_015166.4(MLC1):c.626C>A (p.Ala209Asp)

Gene:

MLC1:modulator of VRAC current 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q13.33

Genomic location:

Preferred name:

NM_015166.4(MLC1):c.626C>A (p.Ala209Asp)

HGVS:

NC_000022.11:g.50074304G>T
NG_009162.1:g.16626C>A
NM_001376472.1:c.626C>A
NM_001376473.1:c.626C>A
NM_001376474.1:c.626C>A
NM_001376475.1:c.626C>A
NM_001376476.1:c.626C>A
NM_001376477.1:c.626C>A
NM_001376478.1:c.626C>A
NM_001376479.1:c.626C>A
NM_001376480.1:c.536C>A
NM_001376481.1:c.524C>A
NM_001376482.1:c.470C>A
NM_001376483.1:c.470C>A
NM_001376484.1:c.389C>A
NM_015166.4:c.626C>AMANE SELECT
NM_139202.3:c.626C>A
NP_001363401.1:p.Ala209Asp
NP_001363402.1:p.Ala209Asp
NP_001363403.1:p.Ala209Asp
NP_001363404.1:p.Ala209Asp
NP_001363405.1:p.Ala209Asp
NP_001363406.1:p.Ala209Asp
NP_001363407.1:p.Ala209Asp
NP_001363408.1:p.Ala209Asp
NP_001363409.1:p.Ala179Asp
NP_001363410.1:p.Ala175Asp
NP_001363411.1:p.Ala157Asp
NP_001363412.1:p.Ala157Asp
NP_001363413.1:p.Ala130Asp
NP_055981.1:p.Ala209Asp
NP_055981.1:p.Ala209Asp
NP_631941.1:p.Ala209Asp
NC_000022.10:g.50512733G>T
NM_015166.3:c.626C>A
NR_164811.1:n.973C>A
NR_164812.1:n.757C>A
NR_164813.1:n.1150C>A

Protein change:

A130D

Molecular consequence:

NM_001376472.1:c.626C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001376473.1:c.626C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001376474.1:c.626C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001376475.1:c.626C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001376476.1:c.626C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001376477.1:c.626C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001376478.1:c.626C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001376479.1:c.626C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001376480.1:c.536C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001376481.1:c.524C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001376482.1:c.470C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001376483.1:c.470C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001376484.1:c.389C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_015166.4:c.626C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_139202.3:c.626C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_164811.1:n.973C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164812.1:n.757C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164813.1:n.1150C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Name:: Megalencephalic leukoencephalopathy with subcortical cysts 1 (MLC1)
Synonyms:: Vacuolating megalencephalic leukoencephalopathy with subcortical cysts; Megalencephaly-cystic leukodystrophy; Leukoencephalopathy with swelling and cysts
Identifiers:: MONDO: MONDO:0024555; MedGen: C5779875; Orphanet: 2478; OMIM: 604004

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002572930	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 1, 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

SCV002572930

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 1, 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	yes	1	not provided	not provided	1	not provided	clinical testing

Citations

PubMed

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 3billion, SCV002572930.1

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

Description

The variant is not observed in the gnomAD v2.1.1 dataset. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.84; 3Cnet: 0.64). Therefore, this variant is classified as uncertain significance according to the recommendation of ACMG/AMP guideline.

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

Last Updated: Nov 11, 2023

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