NM_001256789.3(CACNA1F):c.2234T>C (p.Ile745Thr) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 17, 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:: RCV002512984.2

Allele description [Variation Report for NM_001256789.3(CACNA1F):c.2234T>C (p.Ile745Thr)]

NM_001256789.3(CACNA1F):c.2234T>C (p.Ile745Thr)

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.2234T>C (p.Ile745Thr)

HGVS:

NC_000023.11:g.49222576A>G
NG_009095.2:g.15791T>C
NM_001256789.3:c.2234T>CMANE SELECT
NM_001256790.3:c.2072T>C
NM_005183.4:c.2267T>C
NP_001243718.1:p.Ile745Thr
NP_001243719.1:p.Ile691Thr
NP_005174.2:p.Ile756Thr
NC_000023.10:g.49079035A>G
O60840:p.Ile756Thr

Protein change:

I691T; ILE745THR

Links:

UniProtKB: O60840#VAR_030815; OMIM: 300110.0006; dbSNP: rs122456136

NCBI 1000 Genomes Browser:

rs122456136

Molecular consequence:

NM_001256789.3:c.2234T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001256790.3:c.2072T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_005183.4:c.2267T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Homo sapiens teratocarcinoma-derived growth factor 1, mRNA (cDNA clone MGC:87434...
Homo sapiens teratocarcinoma-derived growth factor 1, mRNA (cDNA clone MGC:87434 IMAGE:5286020), complete cds
gi|45709269|gb|BC067844.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003444658	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 17, 2022)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 15897456, 24051672, 33037074, 15807819, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003444658

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 17, 2022)

germline

clinical testing

PubMed (5)
[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

A CACNA1F mutation identified in an X-linked retinal disorder shifts the voltage dependence of Cav1.4 channel activation.

Hemara-Wahanui A, Berjukow S, Hope CI, Dearden PK, Wu SB, Wilson-Wheeler J, Sharp DM, Lundon-Treweek P, Clover GM, Hoda JC, Striessnig J, Marksteiner R, Hering S, Maw MA.

Proc Natl Acad Sci U S A. 2005 May 24;102(21):7553-8. Epub 2005 May 16.

PubMed [citation]

PMID:: 15897456
PMCID:: PMC1140436

Cav1.4 IT mouse as model for vision impairment in human congenital stationary night blindness type 2.

Knoflach D, Kerov V, Sartori SB, Obermair GJ, Schmuckermair C, Liu X, Sothilingam V, Garcia Garrido M, Baker SA, Glösmann M, Schicker K, Seeliger M, Lee A, Koschak A.

Channels (Austin). 2013 Nov-Dec;7(6):503-13. doi: 10.4161/chan.26368. Epub 2013 Sep 19.

PubMed [citation]

PMID:: 24051672
PMCID:: PMC4042485

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV003444658.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects CACNA1F function (PMID: 15897456, 24051672, 33037074). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 11619). This variant is also known as I745T. This missense change has been observed in individual(s) with congenital stationary night blindness (PMID: 15807819). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 756 of the CACNA1F protein (p.Ile756Thr).

#	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: Jun 29, 2024

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