chr13-30208638-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_032116.5(KATNAL1):​c.1375G>A​(p.Gly459Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts 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

Scores

8
11

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.99
Variant links:
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]

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ACMG classification

Classification made for transcript

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=0.10262972).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KATNAL1NM_032116.5 linkuse as main transcriptc.1375G>A p.Gly459Arg missense_variant 11/11 ENST00000380615.8 NP_115492.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KATNAL1ENST00000380615.8 linkuse as main transcriptc.1375G>A p.Gly459Arg missense_variant 11/111 NM_032116.5 ENSP00000369989 P1
KATNAL1ENST00000380617.7 linkuse as main transcriptc.1375G>A p.Gly459Arg missense_variant 11/112 ENSP00000369991 P1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMar 07, 2023The c.1375G>A (p.G459R) alteration is located in exon 11 (coding exon 10) of the KATNAL1 gene. This alteration results from a G to A substitution at nucleotide position 1375, causing the glycine (G) at amino acid position 459 to be replaced by an arginine (R). 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
0.14
BayesDel_addAF
Uncertain
0.11
D
BayesDel_noAF
Uncertain
-0.080
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.22
T;T
Eigen
Benign
-0.14
Eigen_PC
Benign
0.15
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Uncertain
0.97
.;D
M_CAP
Benign
0.066
D
MetaRNN
Benign
0.10
T;T
MetaSVM
Uncertain
-0.17
T
MutationAssessor
Benign
-0.44
N;N
MutationTaster
Benign
1.0
D;D
PrimateAI
Uncertain
0.70
T
PROVEAN
Benign
1.4
N;N
REVEL
Uncertain
0.37
Sift
Benign
0.37
T;T
Sift4G
Benign
0.40
T;T
Polyphen
0.0020
B;B
Vest4
0.43
MutPred
0.25
Gain of MoRF binding (P = 0.0165);Gain of MoRF binding (P = 0.0165);
MVP
0.27
MPC
0.36
ClinPred
0.67
D
GERP RS
6.2
Varity_R
0.30
gMVP
0.51

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr13-30782775; API