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NM_001378687.1(ATP2C1):c.1818G>T (p.Gln606His) AND Familial benign pemphigus

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 16, 2024
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:
RCV005052220.1

Allele description [Variation Report for NM_001378687.1(ATP2C1):c.1818G>T (p.Gln606His)]

NM_001378687.1(ATP2C1):c.1818G>T (p.Gln606His)

Gene:
ATP2C1:ATPase secretory pathway Ca2+ transporting 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q22.1
Genomic location:
Preferred name:
NM_001378687.1(ATP2C1):c.1818G>T (p.Gln606His)
HGVS:
  • NC_000003.12:g.130980658G>T
  • NG_007379.2:g.135134G>T
  • NM_001001485.3:c.1818G>T
  • NM_001001486.2:c.1818G>T
  • NM_001001487.2:c.1818G>T
  • NM_001199179.3:c.1818G>T
  • NM_001199180.2:c.1920G>T
  • NM_001199181.3:c.1920G>T
  • NM_001199182.2:c.1803G>T
  • NM_001199183.2:c.1770G>T
  • NM_001199184.3:c.1770G>T
  • NM_001199185.2:c.1818G>T
  • NM_001378511.1:c.1920G>T
  • NM_001378512.1:c.1818G>T
  • NM_001378513.1:c.1818G>T
  • NM_001378514.1:c.1770G>T
  • NM_001378687.1:c.1818G>TMANE SELECT
  • NM_014382.5:c.1818G>T
  • NP_001001485.1:p.Gln606His
  • NP_001001486.1:p.Gln606His
  • NP_001001487.1:p.Gln606His
  • NP_001186108.1:p.Gln606His
  • NP_001186109.1:p.Gln640His
  • NP_001186110.1:p.Gln640His
  • NP_001186111.1:p.Gln601His
  • NP_001186112.1:p.Gln590His
  • NP_001186113.1:p.Gln590His
  • NP_001186114.1:p.Gln606His
  • NP_001365440.1:p.Gln640His
  • NP_001365441.1:p.Gln606His
  • NP_001365442.1:p.Gln606His
  • NP_001365443.1:p.Gln590His
  • NP_001365616.1:p.Gln606His
  • NP_055197.2:p.Gln606His
  • NC_000003.11:g.130699502G>T
Protein change:
Q590H
Molecular consequence:
  • NM_001001485.3:c.1818G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001001486.2:c.1818G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001001487.2:c.1818G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001199179.3:c.1818G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001199180.2:c.1920G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001199181.3:c.1920G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001199182.2:c.1803G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001199183.2:c.1770G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001199184.3:c.1770G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001199185.2:c.1818G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378511.1:c.1920G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378512.1:c.1818G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378513.1:c.1818G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378514.1:c.1770G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378687.1:c.1818G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014382.5:c.1818G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Familial benign pemphigus (HHD)
Identifiers:
MONDO: MONDO:0008218; MedGen: C0085106; Orphanet: 2841; OMIM: 169600

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005685271Clinical Genomics Laboratory, Washington University in St. Louis
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Jul 16, 2024) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 Clinical Genomics Laboratory, Washington University in St. Louis, SCV005685271.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

An ATP2C1 c.1818G>T (p.Gln606His) variant was identified at a near heterozygous allelic fraction of 48.5%, a frequency which may be consistent with germline origin. This variant, to our knowledge, has not been reported in the medical literature. This variant is observed on 21/1,613,082 alleles in the general population (gnomAD v.4.1.0). Another variant at thi position, ATP2C1 c.1816C>T (p.Gln606*), which results in a premature termination codon, has been reported in an individual with Hailey-Hailey disease (Dobson-Stone C et al., PMID: 11841554). Computational predictors are uncertain as to the impact of this variant on ATP2C1 function. Due to limited information, and based on ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), the clinical significance of the ATP2C1 c.1818G>T (p.Gln606His) variant is uncertain at this time.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 16, 2025