NM_001830.4(CLCN4):c.1820C>T (p.Pro607Leu) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 6, 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:: RCV001872529.6

Allele description [Variation Report for NM_001830.4(CLCN4):c.1820C>T (p.Pro607Leu)]

NM_001830.4(CLCN4):c.1820C>T (p.Pro607Leu)

Gene:

CLCN4:chloride voltage-gated channel 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp22.2

Genomic location:

Preferred name:

NM_001830.4(CLCN4):c.1820C>T (p.Pro607Leu)

HGVS:

NC_000023.11:g.10213924C>T
NG_012496.1:g.61980C>T
NM_001256944.2:c.1538C>T
NM_001830.4:c.1820C>TMANE SELECT
NP_001243873.1:p.Pro513Leu
NP_001821.2:p.Pro607Leu
NC_000023.10:g.10181964C>T

Protein change:

P513L

Links:

dbSNP: rs1042357480

NCBI 1000 Genomes Browser:

rs1042357480

Molecular consequence:

NM_001256944.2:c.1538C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001830.4:c.1820C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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mPipPyg
mPipPyg
Pipistrellus pygmaeus (soprano pipistrelle), genomic and transcriptomic data

BioProject
NADH dehydrogenase subunit 3, partial (mitochondrion) [Cinclodes fuscus fuscus]
NADH dehydrogenase subunit 3, partial (mitochondrion) [Cinclodes fuscus fuscus]
gi|256807256|gb|ACV29993.1|

Protein
SRP038838 (1)
SRA
alternative protein LAMA1 [Homo sapiens]
alternative protein LAMA1 [Homo sapiens]
gi|444738521|emb|CCQ43326.1|

Protein
Carpophyllum angustifolium ribulose-1,5-bisphosphate carboxylase/oxygenase large...
Carpophyllum angustifolium ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene, partial cds; rbcL-rbcS intergenic spacer, complete sequence; and ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (rbcS) gene, partial cds; plastid
gi|399143619|gb|JN637980.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002125182	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 6, 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

SCV002125182

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 6, 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, SCV002125182.3

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

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 1360558). This variant has not been reported in the literature in individuals affected with CLCN4-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.02%), including at least one homozygous and/or hemizygous individual. This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 607 of the CLCN4 protein (p.Pro607Leu).

#	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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