13-30280183-C-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032116.5(KATNAL1):c.203G>T(p.Ser68Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000000686 in 1,457,954 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
KATNAL1
NM_032116.5 missense
NM_032116.5 missense
Scores
5
14
Clinical Significance
Conservation
PhyloP100: 3.78
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=0.1696226).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KATNAL1 | NM_032116.5 | c.203G>T | p.Ser68Ile | missense_variant | 3/11 | ENST00000380615.8 | NP_115492.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KATNAL1 | ENST00000380615.8 | c.203G>T | p.Ser68Ile | missense_variant | 3/11 | 1 | NM_032116.5 | ENSP00000369989 | P1 | |
KATNAL1 | ENST00000380617.7 | c.203G>T | p.Ser68Ile | missense_variant | 3/11 | 2 | ENSP00000369991 | P1 | ||
KATNAL1 | ENST00000414289.5 | c.203G>T | p.Ser68Ile | missense_variant | 3/4 | 4 | ENSP00000397776 | |||
KATNAL1 | ENST00000441394.1 | c.203G>T | p.Ser68Ile | missense_variant | 3/4 | 3 | ENSP00000407792 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1457954Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 725334
GnomAD4 exome
AF:
AC:
1
AN:
1457954
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
725334
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
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 submitter | clinical testing | Ambry Genetics | Jan 31, 2023 | The c.203G>T (p.S68I) alteration is located in exon 3 (coding exon 2) of the KATNAL1 gene. This alteration results from a G to T substitution at nucleotide position 203, causing the serine (S) at amino acid position 68 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;D;D
REVEL
Benign
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;D;.
Polyphen
B;B;.;.
Vest4
MutPred
Loss of disorder (P = 0.0084);Loss of disorder (P = 0.0084);Loss of disorder (P = 0.0084);Loss of disorder (P = 0.0084);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.