NM_001256789.3(CACNA1F):c.2872C>T (p.Arg958Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 15, 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:: RCV001388118.5

Allele description [Variation Report for NM_001256789.3(CACNA1F):c.2872C>T (p.Arg958Ter)]

NM_001256789.3(CACNA1F):c.2872C>T (p.Arg958Ter)

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.2872C>T (p.Arg958Ter)

HGVS:

NC_000023.11:g.49218511G>A
NG_009095.2:g.19856C>T
NM_001256789.3:c.2872C>TMANE SELECT
NM_001256790.3:c.2710C>T
NM_005183.4:c.2905C>T
NP_001243718.1:p.Arg958Ter
NP_001243719.1:p.Arg904Ter
NP_005174.2:p.Arg969Ter
NC_000023.10:g.49074970G>A
NM_005183.2:c.2905C>T
NM_005183.3:c.2905C>T

Protein change:

R904*; ARG958TER

Links:

OMIM: 300110.0002; dbSNP: rs122456134

NCBI 1000 Genomes Browser:

rs122456134

Molecular consequence:

NM_001256789.3:c.2872C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001256790.3:c.2710C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_005183.4:c.2905C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001588984	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 15, 2022)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 9662399, 11281458, 17525176, 22194652, 24124559, 26992781, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001588984

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 15, 2022)

germline

clinical testing

PubMed (7)
[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

An L-type calcium-channel gene mutated in incomplete X-linked congenital stationary night blindness.

Strom TM, Nyakatura G, Apfelstedt-Sylla E, Hellebrand H, Lorenz B, Weber BH, Wutz K, Gutwillinger N, Rüther K, Drescher B, Sauer C, Zrenner E, Meitinger T, Rosenthal A, Meindl A.

Nat Genet. 1998 Jul;19(3):260-3.

PubMed [citation]

PMID:: 9662399

A summary of 20 CACNA1F mutations identified in 36 families with incomplete X-linked congenital stationary night blindness, and characterization of splice variants.

Boycott KM, Maybaum TA, Naylor MJ, Weleber RG, Robitaille J, Miyake Y, Bergen AA, Pierpont ME, Pearce WG, Bech-Hansen NT.

Hum Genet. 2001 Feb;108(2):91-7.

PubMed [citation]

PMID:: 11281458

See all PubMed Citations (7)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001588984.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. ClinVar contains an entry for this variant (Variation ID: 11615). This variant is also known as p.Arg958*. This premature translational stop signal has been observed in individual(s) with incomplete congenital stationary night blindness (PMID: 9662399). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg969*) in the CACNA1F gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CACNA1F are known to be pathogenic (PMID: 9662399, 11281458, 17525176, 22194652, 24124559, 26992781).

#	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: Oct 8, 2024

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