NM_001256789.3(CACNA1F):c.2998C>T (p.Gln1000Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 4, 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:: RCV002958292.3

Allele description [Variation Report for NM_001256789.3(CACNA1F):c.2998C>T (p.Gln1000Ter)]

NM_001256789.3(CACNA1F):c.2998C>T (p.Gln1000Ter)

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.2998C>T (p.Gln1000Ter)

HGVS:

NC_000023.11:g.49217936G>A
NG_009095.2:g.20431C>T
NM_001256789.3:c.2998C>TMANE SELECT
NM_001256790.3:c.2836C>T
NM_005183.4:c.3031C>T
NP_001243718.1:p.Gln1000Ter
NP_001243719.1:p.Gln946Ter
NP_005174.2:p.Gln1011Ter
NC_000023.10:g.49074395G>A

Protein change:

Q1000*

Molecular consequence:

NM_001256789.3:c.2998C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001256790.3:c.2836C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_005183.4:c.3031C>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
SCV003274211	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 4, 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

SCV003274211

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 4, 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, SCV003274211.2

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

Description

This sequence change creates a premature translational stop signal (p.Gln1011*) 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). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CACNA1F-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

#	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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