NM_016492.5(RANGRF):c.20G>T (p.Cys7Phe) AND Cardiac arrhythmia

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 16, 2023
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:: RCV002654220.10

Allele description [Variation Report for NM_016492.5(RANGRF):c.20G>T (p.Cys7Phe)]

NM_016492.5(RANGRF):c.20G>T (p.Cys7Phe)

Genes:

RANGRF:RAN guanine nucleotide release factor [Gene - OMIM - HGNC]
SLC25A35:solute carrier family 25 member 35 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_016492.5(RANGRF):c.20G>T (p.Cys7Phe)

HGVS:

NC_000017.11:g.8288808G>T
NG_028189.1:g.5158G>T
NM_001177801.2:c.20G>T
NM_001177802.2:c.20G>T
NM_001320871.2:c.*43-376C>A
NM_001330127.2:c.20G>T
NM_016492.5:c.20G>TMANE SELECT
NM_201520.3:c.*808C>A
NP_001171272.1:p.Cys7Phe
NP_001171273.1:p.Cys7Phe
NP_001317056.1:p.Cys7Phe
NP_057576.2:p.Cys7Phe
NC_000017.10:g.8192126G>T
NR_135483.2:n.2353C>A

Protein change:

C7F

Molecular consequence:

NM_201520.3:c.*808C>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001320871.2:c.*43-376C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001177801.2:c.20G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001177802.2:c.20G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001330127.2:c.20G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_016492.5:c.20G>T - missense variant - [Sequence Ontology: SO:0001583]
NR_135483.2:n.2353C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Cardiac arrhythmia
Synonyms:: Cardiac rhythm disease
Identifiers:: EFO: EFO_0004269; MONDO: MONDO:0007263; MedGen: C0003811; Human Phenotype Ontology: HP:0011675

Recent activity

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tatdn2 TatD DNase domain containing 2 [Danio rerio]
tatdn2 TatD DNase domain containing 2 [Danio rerio]
Gene ID:557931

Gene
arhgap29b Rho GTPase activating protein 29b [Danio rerio]
arhgap29b Rho GTPase activating protein 29b [Danio rerio]
Gene ID:378998

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002980545	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 16, 2023)	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

SCV002980545

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 16, 2023)

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002980545.2

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

Description

This variant is present in population databases (rs369657952, gnomAD 0.002%). This sequence change replaces cysteine, which is neutral and slightly polar, with phenylalanine, which is neutral and non-polar, at codon 7 of the RANGRF protein (p.Cys7Phe). This variant has not been reported in the literature in individuals affected with RANGRF-related conditions. 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 output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The phenylalanine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 1947101).

#	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 26, 2024

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