chr11-2445475-A-T

Position:

• chr11-2445475-A-T

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1 PM2 PP3_Moderate PP5

The NM_000218.3(KCNQ1):​c.377A>T​(p.His126Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000139 in 1,442,944 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: KCNQ1 NM_000218.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:1
• Conservation: PhyloP100: 6.46

Genes affected

KCNQ1 (HGNC:6294): (potassium voltage-gated channel subfamily Q member 1) This gene encodes a voltage-gated potassium channel required for repolarization phase of the cardiac action potential. This protein can form heteromultimers with two other potassium channel proteins, KCNE1 and KCNE3. Mutations in this gene are associated with hereditary long QT syndrome 1 (also known as Romano-Ward syndrome), Jervell and Lange-Nielsen syndrome, and familial atrial fibrillation. This gene exhibits tissue-specific imprinting, with preferential expression from the maternal allele in some tissues, and biallelic expression in others. This gene is located in a region of chromosome 11 amongst other imprinted genes that are associated with Beckwith-Wiedemann syndrome (BWS), and itself has been shown to be disrupted by chromosomal rearrangements in patients with BWS. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

• PM1: In a transmembrane_region Helical; Name=Segment S1 (size 20) in uniprot entity KCNQ1_HUMAN there are 12 pathogenic changes around while only 1 benign (92%) in NM_000218.3
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.92
• PP5: Variant 11-2445475-A-T is Pathogenic according to our data. Variant chr11-2445475-A-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 200911.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=1, Uncertain_significance=1}. Variant chr11-2445475-A-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCNQ1	NM_000218.3	c.377A>T	p.His126Leu	missense_variant	1/16	ENST00000155840.12	NP_000209.2
KCNQ1	NM_001406836.1	c.377A>T	p.His126Leu	missense_variant	1/15		NP_001393765.1
KCNQ1	NM_001406838.1	c.377A>T	p.His126Leu	missense_variant	1/11		NP_001393767.1
KCNQ1	NM_001406837.1	c.15A>T	p.Pro5=	synonymous_variant	1/17		NP_001393766.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNQ1	ENST00000155840.12	c.377A>T	p.His126Leu	missense_variant	1/16	1	NM_000218.3	ENSP00000155840	P1
KCNQ1	ENST00000345015.4	n.154A>T		non_coding_transcript_exon_variant	1/3	1
KCNQ1	ENST00000496887.7	c.116A>T	p.His39Leu	missense_variant	2/16	5		ENSP00000434560
KCNQ1	ENST00000646564.2	c.377A>T	p.His126Leu	missense_variant	1/11			ENSP00000495806

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000139 AC: 2 AN: 1442944 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 717972

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000540

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Aug 25, 2011

This missense change is denoted His126Leu (aka H126L) at the protein level and c.377 A>T at the cDNA level. The His126Leu variant in the KCNQ1 gene has not been reported previously as a disease-causing mutation nor as a benign polymorphism, to our knowledge. His126Leu results in a non-conservative amino acid substitution of a positively charged Histidine with a non-polar Leucine at a residue that is conserved across species. As a result, in silico analysis predicts His126Leu is probably damaging to the protein structure/function (Adzhubei IA et al., 2010, Schwarz JM et al., 2011). In addition, mutations in nearby codons (Cys122Tyr, Phe127Leu) have been reported in association with LQTS, supporting the functional importance of this region of the protein. Furthermore, the His126Leu variant was not detected in 470 alleles from control individuals of various ethnic backgrounds tested at GeneDx, indicating it is not a common benign variant. In summary, while the His126Leu variant is a good candidate for a disease-causing mutation, we cannot unequivocally determine the clinical significance of this variant with the clinical and molecular information available at this time. The variant is found in LQT panel(s). -

Long QT syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Sep 27, 2017

This variant identified in the KCNQ1 gene is located in the transmembrane S1 region of the resulting protein (PMID: 19841300, 25348405). For more information about the location of this variant, please visit www.invitae.com/KCNQ1-topology. It is unclear how this variant impacts the function of this protein. 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 (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with KCNQ1-related disease. ClinVar contains an entry for this variant (Variation ID: 200911). This variant is not present in population databases (ExAC no frequency). This sequence change replaces histidine with leucine at codon 126 of the KCNQ1 protein (p.His126Leu). The histidine residue is highly conserved and there is a moderate physicochemical difference between histidine and leucine. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.98
BayesDel_addAF	Pathogenic	0.46	D
BayesDel_noAF	Pathogenic	0.43
CADD	Pathogenic	30
DANN	Benign	0.96
DEOGEN2	Pathogenic	0.96	.;D;.
Eigen	Uncertain	0.66
Eigen_PC	Uncertain	0.54
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.86	D;D;D
M_CAP	Pathogenic	0.86	D
MetaRNN	Pathogenic	0.92	D;D;D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Uncertain	2.0	.;M;.
MutationTaster	Benign	1.0	D
PrimateAI	Pathogenic	0.80	D
PROVEAN	Pathogenic	-8.1	D;D;.
REVEL	Pathogenic	0.89
Sift	Pathogenic	0.0	D;D;.
Sift4G	Uncertain	0.0030	D;D;.
Polyphen		1.0	.;D;.
Vest4		0.85
MutPred		0.54		.;Loss of helix (P = 0.1299);.;
MVP		0.99
MPC		2.5
ClinPred		1.0	D
GERP RS		3.2
Varity_R		0.99
gMVP		0.98

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs794728579; hg19: chr11-2466705;