NM_015353.3:c.92C>T

Variant names:

• chr17-75047342-C-T
• rs943935861
• NM_015353.3:c.92C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_015353.3(KCTD2):​c.92C>T​(p.Pro31Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000147 in 1,154,298 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.000067 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0000070 (0 hom.)
• Consequence: KCTD2 NM_015353.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.40
• 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: Likely_benign. The variant received -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.16308632).

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.92C>T	p.Pro31Leu	missense	Exon 1 of 6	NP_056168.1	Q14681
	KCTD2	NR_110834.2		n.75+43C>T		intron	N/A
	KCTD2	NR_110835.2		n.366-1878C>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.92C>T	p.Pro31Leu	missense	Exon 1 of 6	ENSP00000312814.6	Q14681
	KCTD2	ENST00000581589.5	TSL:1	c.-258-1878C>T		intron	N/A	ENSP00000464630.1	J3QSC8
	KCTD2	ENST00000375286.7	TSL:1	n.49+43C>T		intron	N/A	ENSP00000364435.3	H0Y3B9

Frequencies

GnomAD3 genomes AF: 0.0000669 AC: 10 AN: 149532 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000243

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000697 AC: 7 AN: 1004658 Hom.: 0 Cov.: 31 AF XY: 0.00000423 AC XY: 2 AN XY: 473168

African (AFR) AF: 0.000350 AC: 7 AN: 19978

American (AMR) AF: 0.00 AC: 0 AN: 6066

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10994

East Asian (EAS) AF: 0.00 AC: 0 AN: 19480

South Asian (SAS) AF: 0.00 AC: 0 AN: 18912

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 17268

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2478

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 871326

Other (OTH) AF: 0.00 AC: 0 AN: 38156

GnomAD4 genome AF: 0.0000668 AC: 10 AN: 149640 Hom.: 0 Cov.: 31 AF XY: 0.0000411 AC XY: 3 AN XY: 73034

African (AFR) AF: 0.000243 AC: 10 AN: 41234

American (AMR) AF: 0.00 AC: 0 AN: 15068

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3442

East Asian (EAS) AF: 0.00 AC: 0 AN: 5134

South Asian (SAS) AF: 0.00 AC: 0 AN: 4816

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9598

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67062

Other (OTH) AF: 0.00 AC: 0 AN: 2086

Alfa AF: 0.000214 Hom.: 0

Bravo AF: 0.000144

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	0.088
BayesDel_addAF	Benign	-0.16	T
BayesDel_noAF	Benign	-0.46
CADD	Benign	22
DANN	Benign	0.89
DEOGEN2	Benign	0.010	T
Eigen	Benign	-0.73
Eigen_PC	Benign	-0.65
FATHMM_MKL	Benign	0.58	D
LIST_S2	Benign	0.60	T
M_CAP	Pathogenic	0.66	D
MetaRNN	Benign	0.16	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.55	N
PhyloP100		2.4
PrimateAI	Pathogenic	0.88	D
PROVEAN	Benign	-0.82	N
REVEL	Benign	0.073
Sift	Uncertain	0.0030	D
Sift4G	Benign	0.24	T
Polyphen		0.063	B
Vest4		0.19
MutPred		0.34		Loss of glycosylation at P31 (P = 0.0352)
MVP		0.38
MPC		1.0
ClinPred		0.62	D
GERP RS		1.6
PromoterAI		-0.075	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.11
gMVP		0.30
Mutation Taster		=89/11	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: rs943935861; hg19: chr17-73043437;