rs560695692

Variant names:

• chr15-65077695-C-A
• rs560695692
• NM_001101362.3:c.880C>A

Your query was ambiguous. Multiple possible variants found:

• chr15-65077695-C-A
• chr15-65077695-C-G

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2 PP3

The NM_001101362.3(KBTBD13):​c.880C>A​(p.Pro294Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000014 in 1,424,676 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P294A) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 34)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: KBTBD13 NM_001101362.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.64

Genes affected

KBTBD13 (HGNC:37227): (kelch repeat and BTB domain containing 13) The gene belongs to a family of genes encoding proteins containing a BTB domain and several kelch repeats. The BTB domain functions as a protein-protein interaction module, which includes an ability to self-associate or to interact with non-BTB domain-containing proteins. The kelch motif typically occurs in groups of five to seven repeats, and has been found in proteins with diverse functions. Known functions of these family members include transcription regulation, ion channel tetramerization and gating, protein ubiquitination or degradation, and cytoskeleton regulation. The exact function of this family member has yet to be determined. [provided by RefSeq, Jun 2010]

ACMG classification

Our verdict: Uncertain_significance. The variant received 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.802

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KBTBD13	NM_001101362.3	c.880C>A	p.Pro294Thr	missense_variant	Exon 1 of 1	ENST00000432196.5	NP_001094832.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KBTBD13	ENST00000432196.5	c.880C>A	p.Pro294Thr	missense_variant	Exon 1 of 1	6	NM_001101362.3	ENSP00000388723.2

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 0.00000140 AC: 2 AN: 1424676 Hom.: 0 Cov.: 83 AF XY: 0.00 AC XY: 0 AN XY: 706640

Gnomad4 AFR exome AF: 0.00 AC: 0 AN: 32718

Gnomad4 AMR exome AF: 0.00 AC: 0 AN: 41218

Gnomad4 ASJ exome AF: 0.00 AC: 0 AN: 25074

Gnomad4 EAS exome AF: 0.00 AC: 0 AN: 38740

Gnomad4 SAS exome AF: 0.00 AC: 0 AN: 83104

Gnomad4 FIN exome AF: 0.00 AC: 0 AN: 40246

Gnomad4 NFE exome AF: 0.00000182 AC: 2 AN: 1099052

Gnomad4 Remaining exome AF: 0.00 AC: 0 AN: 59004

GnomAD4 genome Cov.: 34

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Pathogenic	0.20	D
BayesDel_noAF	Uncertain	0.060
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.18	T
Eigen	Uncertain	0.55
Eigen_PC	Uncertain	0.53
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Benign	0.78	T
M_CAP	Pathogenic	0.47	D
MetaRNN	Pathogenic	0.80	D
MetaSVM	Benign	-0.36	T
MutationAssessor	Uncertain	2.3	M
PrimateAI	Uncertain	0.77	T
PROVEAN	Pathogenic	-4.7	D
REVEL	Uncertain	0.44
Sift	Uncertain	0.0080	D
Sift4G	Benign	0.065	T
Polyphen		0.99	D
Vest4		0.66
MutPred		0.50		Loss of sheet (P = 0.1158);
MVP		0.50
MPC		1.4
ClinPred		0.97	D
GERP RS		5.3
Varity_R		0.70
gMVP		0.59
Mutation Taster		=74/26	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

Publications

LitVar

Other links and lift over

dbSNP: rs560695692; hg19: chr15-65370033;