NM_005477.3:c.1444G>A

Variant names:

• chr15-73329719-C-T
• rs794727637
• NM_005477.3:c.1444G>A

Variant summary

Our verdict is Pathogenic. The variant received 22 ACMG points: 22P and 0B. PS1 PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_005477.3(HCN4):​c.1444G>A​(p.Gly482Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Pathogenic in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G482E) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 34)
• Consequence: HCN4 NM_005477.3 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:4
• Conservation: PhyloP100: 7.81
• Publications: 21 publications found

Genes affected

HCN4 (HGNC:16882): (hyperpolarization activated cyclic nucleotide gated potassium channel 4) This gene encodes a member of the hyperpolarization-activated cyclic nucleotide-gated potassium channels. The encoded protein shows slow kinetics of activation and inactivation, and is necessary for the cardiac pacemaking process. This channel may also mediate responses to sour stimuli. Mutations in this gene have been linked to sick sinus syndrome 2, also known as atrial fibrillation with bradyarrhythmia or familial sinus bradycardia. Two pseudogenes have been identified on chromosome 15. [provided by RefSeq, Oct 2008]

HCN4 Gene-Disease associations (from GenCC):

• sick sinus syndrome 2, autosomal dominant

  Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Ambry Genetics
• Brugada syndrome 8

  Inheritance: AD Classification: MODERATE, LIMITED Submitted by: Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
• familial sick sinus syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• familial thoracic aortic aneurysm and aortic dissection

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen
• Brugada syndrome 1

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Pathogenic. The variant received 22 ACMG points.

• PS1: Transcript NM_005477.3 (HCN4) is affected with MISSENSE_VARIANT having same AA change as one Pathogenic present in ClinVar.
• PM1: In a hotspot region, there are 7 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 12 uncertain in NM_005477.3
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr15-73329718-C-T is described in ClinVar as Likely_pathogenic. ClinVar VariationId is 1675065.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.993
• PP5: Variant 15-73329719-C-T is Pathogenic according to our data. Variant chr15-73329719-C-T is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 197253.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCN4	NM_005477.3	c.1444G>A	p.Gly482Arg	missense_variant	Exon 4 of 8	ENST00000261917.4	NP_005468.1
HCN4	XM_011521148.3	c.226G>A	p.Gly76Arg	missense_variant	Exon 3 of 7		XP_011519450.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCN4	ENST00000261917.4	c.1444G>A	p.Gly482Arg	missense_variant	Exon 4 of 8	1	NM_005477.3	ENSP00000261917.3

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 34

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:2

Oct 30, 2022

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Observed in multiple unrelated patients in association with bradycardia, LVNC, sinus node dysfunction, and/or non-compaction cardiomyopathy referred for genetic testing at GeneDx and in the published literature (Millat et al., 2015; Schweizer et al., 2014; Ishikawa et al., 2017); Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies showed that p.(G482R) mutant subunits were non-functional and showed a dominant-negative effect on the channel current (Milano et al., 2014; Schweizer et al., 2014); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 25145519, 25642760, 27173043, 26206080, 28104484, 26688388, 30471092, 32577394, 34088380, 25145517, 25145518, 35328031, 33185997) -

Jun 09, 2016

Eurofins Ntd Llc (ga)

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Brugada syndrome 8 Pathogenic:1

Nov 19, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 482 of the HCN4 protein (p.Gly482Arg). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with sinus node dysfunction and left ventricular non compaction (PMID: 25145517, 25145518, 26206080, 27173043). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 197253). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt HCN4 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects HCN4 function (PMID: 25145518). For these reasons, this variant has been classified as Pathogenic. -

Cardiovascular phenotype Pathogenic:1

Aug 27, 2021

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.G482R pathogenic mutation (also known as c.1444G>A), located in coding exon 4 of the HCN4 gene, results from a G to A substitution at nucleotide position 1444. The glycine at codon 482 is replaced by arginine, an amino acid with dissimilar properties. This alteration has been reported in multiple individuals with sinus bradycardia and left ventricular non-compaction (LVNC) (Schweizer PA et al. J Am Coll Cardiol, 2014 Aug;64:757-67; Millat G et al. Eur J Med Genet, 2015 Sep;58:439-42; Chanavat V et al. Clin Chim Acta, 2016 Jan;453:80-5; Ishikawa T et al. Heart Rhythm, 2017 05;14:717-724; Hanania HL et al. Circ Genom Precis Med, 2019 12;12:e002626; Richard P et al. Clin Genet, 2019 03;95:356-367; Wacker-Gussmann A et al. HeartRhythm Case Rep, 2020 Jun;6:352-356). In vitro studies demonstrated that this alteration may impact protein function (Schweizer PA et al. J Am Coll Cardiol, 2014 Aug;64:757-67). Further, a different alteration located at the same position, resulting in the same protein change, c.1444G>C (p.G428R), has been reported in affected individuals and was found to segregate with disease in a family (Milano A et al. J Am Coll Cardiol, 2014 Aug;64:745-56). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This missense alteration is located in a region that has a low rate of benign missense variation (Lek M et al. Nature. 2016 Aug 18;536(7616):285-91; DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources. Firth H.V. et al. 2009. Am.J.Hum.Genet. 84, 524-533 (DOI: dx.doi.org/10/1016/j.ajhg.2009.03.010)). In addition, this alteration is predicted to be deleterious by BayesDel in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.57	D
BayesDel_noAF	Pathogenic	0.58
CADD	Uncertain	26
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.98	D
Eigen	Uncertain	0.62
Eigen_PC	Uncertain	0.45
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Pathogenic	1.0	D
M_CAP	Pathogenic	0.88	D
MetaRNN	Pathogenic	0.99	D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Pathogenic	3.4	M
PhyloP100		7.8
PrimateAI	Pathogenic	0.82	D
PROVEAN	Pathogenic	-7.7	D
REVEL	Pathogenic	0.97
Sift	Uncertain	0.0010	D
Sift4G	Pathogenic	0.0010	D
Polyphen		1.0	D
Vest4		0.99
MutPred		0.85		Gain of MoRF binding (P = 0.057);
MVP		0.93
MPC		1.3
ClinPred		1.0	D
GERP RS		4.2
Varity_R		0.85
gMVP		0.99
Mutation Taster		=3/97	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs794727637; hg19: chr15-73622060;