NM_015353.3:c.143C>T

Variant names:

• chr17-75047393-C-T
• rs1411415760
• NM_015353.3:c.143C>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_015353.3(KCTD2):​c.143C>T​(p.Ala48Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000139 in 1,153,560 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.000020 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000013 (0 hom.)
• Consequence: KCTD2 NM_015353.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.183
• Publications: 0 publications found

Genes affected

KCTD2 (HGNC:21294): (potassium channel tetramerization domain containing 2) Predicted to enable cullin family protein binding activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Predicted to be part of Cul3-RING ubiquitin ligase complex. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ATP5PD (HGNC:845): (ATP synthase peripheral stalk subunit d) Mitochondrial ATP synthase catalyzes ATP synthesis, utilizing an electrochemical gradient of protons across the inner membrane during oxidative phosphorylation. It is composed of two linked multi-subunit complexes: the soluble catalytic core, F1, and the membrane-spanning component, Fo, which comprises the proton channel. The F1 complex consists of 5 different subunits (alpha, beta, gamma, delta, and epsilon) assembled in a ratio of 3 alpha, 3 beta, and a single representative of the other 3. The Fo seems to have nine subunits (a, b, c, d, e, f, g, F6 and 8). This gene encodes the d subunit of the Fo complex. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. In addition, three pseudogenes are located on chromosomes 9, 12 and 15. [provided by RefSeq, Jun 2010]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.14449656).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015353.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCTD2	NM_015353.3	MANE Select	c.143C>T	p.Ala48Val	missense	Exon 1 of 6	NP_056168.1	Q14681
	KCTD2	NR_110834.2		n.76-26C>T		intron	N/A
	KCTD2	NR_110835.2		n.366-1827C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCTD2	ENST00000322444.7	TSL:1 MANE Select	c.143C>T	p.Ala48Val	missense	Exon 1 of 6	ENSP00000312814.6	Q14681
	KCTD2	ENST00000581589.5	TSL:1	c.-258-1827C>T		intron	N/A	ENSP00000464630.1	J3QSC8
	KCTD2	ENST00000375286.7	TSL:1	n.50-26C>T		intron	N/A	ENSP00000364435.3	H0Y3B9

Frequencies

GnomAD3 genomes AF: 0.0000134 AC: 2 AN: 149148 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000668

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000129 AC: 13 AN: 1004304 Hom.: 0 Cov.: 31 AF XY: 0.0000169 AC XY: 8 AN XY: 474188

African (AFR) AF: 0.00 AC: 0 AN: 20016

American (AMR) AF: 0.00 AC: 0 AN: 5992

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10862

East Asian (EAS) AF: 0.00 AC: 0 AN: 19052

South Asian (SAS) AF: 0.000211 AC: 4 AN: 18928

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 17204

Middle Eastern (MID) AF: 0.000399 AC: 1 AN: 2506

European-Non Finnish (NFE) AF: 0.00000574 AC: 5 AN: 871758

Other (OTH) AF: 0.0000790 AC: 3 AN: 37986

GnomAD4 genome AF: 0.0000201 AC: 3 AN: 149256 Hom.: 0 Cov.: 31 AF XY: 0.0000137 AC XY: 1 AN XY: 72822

African (AFR) AF: 0.00 AC: 0 AN: 41228

American (AMR) AF: 0.0000667 AC: 1 AN: 14986

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3412

East Asian (EAS) AF: 0.00 AC: 0 AN: 5146

South Asian (SAS) AF: 0.00 AC: 0 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9526

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 66858

Other (OTH) AF: 0.000481 AC: 1 AN: 2078

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000113

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.089
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.58
CADD	Benign	16
DANN	Uncertain	0.99
DEOGEN2	Benign	0.0046	T
Eigen	Benign	-0.82
Eigen_PC	Benign	-0.80
FATHMM_MKL	Benign	0.14	N
LIST_S2	Benign	0.50	T
M_CAP	Pathogenic	0.39	D
MetaRNN	Benign	0.14	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.34	N
PhyloP100		-0.18
PrimateAI	Pathogenic	0.88	D
PROVEAN	Benign	-0.26	N
REVEL	Benign	0.10
Sift	Benign	0.16	T
Sift4G	Benign	0.068	T
Polyphen		0.0080	B
Vest4		0.089
MutPred		0.38		Gain of sheet (P = 0.0344)
MVP		0.41
MPC		1.0
ClinPred		0.15	T
GERP RS		3.5
PromoterAI		-0.020	Neutral
Varity_R		0.079
gMVP		0.36
Mutation Taster		=87/13	polymorphism

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

Other links and lift over

dbSNP: rs1411415760; hg19: chr17-73043488;