NM_012284.3:c.1068C>A

Variant names:

• chr12-49544261-C-A
• rs149749663
• NM_012284.3:c.1068C>A

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2 PP3_Strong

The NM_012284.3(KCNH3):​c.1068C>A​(p.Ser356Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: KCNH3 NM_012284.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378

Genes affected

KCNH3 (HGNC:6252): (potassium voltage-gated channel subfamily H member 3) The protein encoded by this gene is a voltage-gated potassium channel alpha subunit predominantly expressed in the forebrain. Studies in mice have found that cognitive function increases when this gene is knocked out. In humans, the encoded protein has been shown to be capable of binding glycoprotein 120 of the human immunodeficiency virus type 1 (HIV-1) envelope. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2015]

ACMG classification

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.979

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCNH3	NM_012284.3	c.1068C>A	p.Ser356Arg	missense_variant	Exon 7 of 15	ENST00000257981.7	NP_036416.1
KCNH3	NM_001314030.2	c.888C>A	p.Ser296Arg	missense_variant	Exon 7 of 15		NP_001300959.1
KCNH3	XM_011538085.3	c.1068C>A	p.Ser356Arg	missense_variant	Exon 7 of 15		XP_011536387.1
KCNH3	XM_047428613.1	c.1068C>A	p.Ser356Arg	missense_variant	Exon 7 of 10		XP_047284569.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCNH3	ENST00000257981.7	c.1068C>A	p.Ser356Arg	missense_variant	Exon 7 of 15	1	NM_012284.3	ENSP00000257981.5
KCNH3	ENST00000551415.1	n.8C>A		non_coding_transcript_exon_variant	Exon 1 of 2	3
KCNH3	ENST00000649994.1	n.*678C>A		non_coding_transcript_exon_variant	Exon 8 of 16			ENSP00000497890.1
KCNH3	ENST00000649994.1	n.*678C>A		3_prime_UTR_variant	Exon 8 of 16			ENSP00000497890.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 37

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.44	D
BayesDel_noAF	Pathogenic	0.40
CADD	Benign	15
DANN	Uncertain	0.99
DEOGEN2	Pathogenic	0.86	D
Eigen	Benign	-0.62
Eigen_PC	Benign	-0.93
FATHMM_MKL	Benign	0.43	N
LIST_S2	Uncertain	0.97	D
M_CAP	Pathogenic	0.65	D
MetaRNN	Pathogenic	0.98	D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Pathogenic	3.2	M
PrimateAI	Pathogenic	0.82	D
PROVEAN	Pathogenic	-4.6	D
REVEL	Pathogenic	0.74
Sift	Uncertain	0.0050	D
Sift4G	Uncertain	0.0040	D
Polyphen		0.99	D
Vest4		0.93
MutPred		0.80		Gain of methylation at S356 (P = 0.0283);
MVP		1.0
MPC		2.4
ClinPred		1.0	D
GERP RS		-6.2
Varity_R		0.71
gMVP		0.96

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs149749663; hg19: chr12-49938044;