NM_021098.3(CACNA1H):c.6311_6325del (p.Ile2104_Cys2109delinsSer) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 14, 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:: RCV000635020.6

Allele description [Variation Report for NM_021098.3(CACNA1H):c.6311_6325del (p.Ile2104_Cys2109delinsSer)]

NM_021098.3(CACNA1H):c.6311_6325del (p.Ile2104_Cys2109delinsSer)

Gene:

CACNA1H:calcium voltage-gated channel subunit alpha1 H [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_021098.3(CACNA1H):c.6311_6325del (p.Ile2104_Cys2109delinsSer)

HGVS:

NC_000016.10:g.1220243_1220257del
NG_012647.1:g.72003_72017del
NM_001005407.2:c.6293_6307del
NM_021098.3:c.6311_6325delMANE SELECT
NP_001005407.1:p.Ile2098_Cys2103delinsSer
NP_066921.2:p.Ile2104_Cys2109delinsSer
NC_000016.9:g.1270243_1270257del
NM_021098.2:c.6311_6325delTCACCAGCTCCGCCT

Links:

dbSNP: rs774660673

NCBI 1000 Genomes Browser:

rs774660673

Molecular consequence:

NM_001005407.2:c.6293_6307del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_021098.3:c.6311_6325del - inframe_indel - [Sequence Ontology: SO:0001820]

Condition(s)

Name:: Idiopathic generalized epilepsy
Synonyms:: EIG; Generalised epilepsy
Identifiers:: MONDO: MONDO:0005579; MedGen: C0270850; OMIM: 600669; OMIM: PS600669

Name:: Hyperaldosteronism, familial, type IV (HALD4)
Synonyms:: FH IV; ALDOSTERONISM, PRIMARY, AND HYPERTENSION
Identifiers:: MONDO: MONDO:0014875; MedGen: C4310756; OMIM: 617027

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000756398	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 14, 2024)	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

SCV000756398

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 14, 2024)

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000756398.6

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

Description

This variant, c.6311_6325del, is a complex sequence change that results in the deletion of 6 and insertion of 1 amino acid(s) in the CACNA1H protein (p.Ile2104_Cys2109delinsSer). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with CACNA1H-related conditions. ClinVar contains an entry for this variant (Variation ID: 529561). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

#	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: Mar 5, 2024

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