NM_001256789.3(CACNA1F):c.2968G>C (p.Gly990Arg) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 30, 2020
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:: RCV001945656.5

Allele description [Variation Report for NM_001256789.3(CACNA1F):c.2968G>C (p.Gly990Arg)]

NM_001256789.3(CACNA1F):c.2968G>C (p.Gly990Arg)

Gene:

CACNA1F:calcium voltage-gated channel subunit alpha1 F [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp11.23

Genomic location:

Preferred name:

NM_001256789.3(CACNA1F):c.2968G>C (p.Gly990Arg)

HGVS:

NC_000023.11:g.49217966C>G
NG_009095.2:g.20401G>C
NM_001256789.3:c.2968G>CMANE SELECT
NM_001256790.3:c.2806G>C
NM_005183.4:c.3001G>C
NP_001243718.1:p.Gly990Arg
NP_001243719.1:p.Gly936Arg
NP_005174.2:p.Gly1001Arg
NC_000023.10:g.49074425C>G

Protein change:

G1001R

Links:

dbSNP: rs782473510

NCBI 1000 Genomes Browser:

rs782473510

Molecular consequence:

NM_001256789.3:c.2968G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001256790.3:c.2806G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_005183.4:c.3001G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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R-spondin-3 isoform X1 [Homo sapiens]
R-spondin-3 isoform X1 [Homo sapiens]
gi|1034651932|ref|XP_016866867.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002191713	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 30, 2020)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 22735794, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002191713

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 30, 2020)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Mutation screening of TRPM1, GRM6, NYX and CACNA1F genes in patients with congenital stationary night blindness.

Wang Q, Gao Y, Li S, Guo X, Zhang Q.

Int J Mol Med. 2012 Sep;30(3):521-6. doi: 10.3892/ijmm.2012.1039. Epub 2012 Jun 20.

PubMed [citation]

PMID:: 22735794

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, SCV002191713.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

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 disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has been observed in individual(s) with congenital stationary night blindness (PMID: 22735794). This variant is not present in population databases (ExAC no frequency). This sequence change replaces glycine with arginine at codon 1001 of the CACNA1F protein (p.Gly1001Arg). The glycine residue is highly conserved and there is a moderate physicochemical difference between glycine and arginine.

#	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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