chr13-30208640-T-A

Position:

• chr13-30208640-T-A

Variant summary

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

The NM_032116.5(KATNAL1):​c.1373A>T​(p.Lys458Ile) 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. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: KATNAL1 NM_032116.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.128

Genes affected

KATNAL1 (HGNC:28361): (katanin catalytic subunit A1 like 1) Enables identical protein binding activity and microtubule-severing ATPase activity. Involved in microtubule severing. Located in cytoplasm; microtubule; and spindle pole. [provided by Alliance of Genome Resources, Apr 2022]

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=0.112888396).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KATNAL1	NM_032116.5	c.1373A>T	p.Lys458Ile	missense_variant	11/11	ENST00000380615.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KATNAL1	ENST00000380615.8	c.1373A>T	p.Lys458Ile	missense_variant	11/11	1	NM_032116.5	P1
KATNAL1	ENST00000380617.7	c.1373A>T	p.Lys458Ile	missense_variant	11/11	2		P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 23, 2023

The c.1373A>T (p.K458I) alteration is located in exon 11 (coding exon 10) of the KATNAL1 gene. This alteration results from a A to T substitution at nucleotide position 1373, causing the lysine (K) at amino acid position 458 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Uncertain	0.082	D
BayesDel_noAF	Benign	-0.12
CADD	Benign	17
DANN	Uncertain	0.98
DEOGEN2	Benign	0.24	T;T
Eigen	Benign	-0.75
Eigen_PC	Benign	-0.63
FATHMM_MKL	Benign	0.71	D
LIST_S2	Uncertain	0.89	.;D
M_CAP	Benign	0.049	D
MetaRNN	Benign	0.11	T;T
MetaSVM	Uncertain	-0.16	T
MutationAssessor	Benign	-0.49	N;N
MutationTaster	Benign	0.79	N;N
PrimateAI	Benign	0.30	T
PROVEAN	Benign	-0.11	N;N
REVEL	Uncertain	0.37
Sift	Benign	0.094	T;T
Sift4G	Benign	0.29	T;T
Polyphen		0.0	B;B
Vest4		0.36
MutPred		0.50		Loss of disorder (P = 0.0096);Loss of disorder (P = 0.0096);
MVP		0.47
MPC		0.57
ClinPred		0.65	D
GERP RS		-4.3
Varity_R		0.091
gMVP		0.46

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: rs1873372454; hg19: chr13-30782777;