chr16-57744439-A-C

Position:

• chr16-57744439-A-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_005886.3(KATNB1):​c.217A>C​(p.Thr73Pro) 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 benign outcome for this variant. 13/21 in silico tools predict a benign 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. T73A) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: KATNB1 NM_005886.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.91

Genes affected

KATNB1 (HGNC:6217): (katanin regulatory subunit B1) Microtubules, polymers of alpha and beta tubulin subunits, form the mitotic spindle of a dividing cell and help to organize membranous organelles during interphase. Katanin is a heterodimer that consists of a 60 kDa ATPase (p60 subunit A 1) and an 80 kDa accessory protein (p80 subunit B 1). The p60 subunit acts to sever and disassemble microtubules, while the p80 subunit targets the enzyme to the centrosome. Katanin is a member of the AAA family of ATPases. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.080756515).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KATNB1	NM_005886.3	c.217A>C	p.Thr73Pro	missense_variant	4/20	ENST00000379661.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KATNB1	ENST00000379661.8	c.217A>C	p.Thr73Pro	missense_variant	4/20	5	NM_005886.3	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.075
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.43
CADD	Benign	20
DANN	Uncertain	0.98
DEOGEN2	Benign	0.015	T;T;T;T;.
Eigen	Benign	-0.48
Eigen_PC	Benign	-0.19
FATHMM_MKL	Uncertain	0.82	D
LIST_S2	Benign	0.56	T;T;T;T;T
M_CAP	Benign	0.0041	T
MetaRNN	Benign	0.081	T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-2.3	N;.;.;.;.
MutationTaster	Benign	0.67	D
PrimateAI	Uncertain	0.53	T
PROVEAN	Benign	-0.44	N;N;N;N;N
REVEL	Benign	0.12
Sift	Benign	0.22	T;T;T;T;T
Sift4G	Benign	0.65	T;T;T;T;T
Polyphen		0.0020	B;.;.;.;.
Vest4		0.27
MutPred		0.46		Loss of phosphorylation at T73 (P = 0.0506);Loss of phosphorylation at T73 (P = 0.0506);.;Loss of phosphorylation at T73 (P = 0.0506);Loss of phosphorylation at T73 (P = 0.0506);
MVP		0.41
MPC		0.65
ClinPred		0.19	T
GERP RS		5.5
Varity_R		0.090
gMVP		0.33

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs145567409; hg19: chr16-57778351;