2-200469989-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate

The NM_001100423.2(SPATS2L):​c.1033A>G​(p.Lys345Glu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

SPATS2L
NM_001100423.2 missense

Scores

6
10
3

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.84
Variant links:
Genes affected
SPATS2L (HGNC:24574): (spermatogenesis associated serine rich 2 like) Enables RNA binding activity. Located in cytosol; nucleolus; and nucleoplasm. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.926

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SPATS2LNM_001100423.2 linkuse as main transcriptc.1033A>G p.Lys345Glu missense_variant 11/13 ENST00000409140.8 NP_001093893.1
LOC101927741XR_007088047.1 linkuse as main transcriptn.569+6114T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SPATS2LENST00000409140.8 linkuse as main transcriptc.1033A>G p.Lys345Glu missense_variant 11/132 NM_001100423.2 ENSP00000386730 P1Q9NUQ6-1
ENST00000655656.1 linkuse as main transcriptn.566+6114T>C intron_variant, non_coding_transcript_variant

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 GeneticsJul 25, 2023The c.1033A>G (p.K345E) alteration is located in exon 11 (coding exon 9) of the SPATS2L gene. This alteration results from a A to G substitution at nucleotide position 1033, causing the lysine (K) at amino acid position 345 to be replaced by a glutamic acid (E). 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
Pathogenic
0.58
BayesDel_addAF
Pathogenic
0.34
D
BayesDel_noAF
Pathogenic
0.24
CADD
Pathogenic
28
DANN
Uncertain
1.0
DEOGEN2
Benign
0.27
T;T;T;T;T;.;T;.;.
Eigen
Pathogenic
0.69
Eigen_PC
Uncertain
0.66
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.93
.;.;.;D;.;D;D;D;D
M_CAP
Benign
0.015
T
MetaRNN
Pathogenic
0.93
D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
-0.21
T
MutationAssessor
Uncertain
2.6
M;M;M;.;M;.;M;.;.
MutationTaster
Benign
0.99
D;D;D;D;D;D;D;D;D
PrimateAI
Uncertain
0.76
T
PROVEAN
Uncertain
-2.6
D;D;D;D;D;D;D;.;D
REVEL
Uncertain
0.49
Sift
Uncertain
0.013
D;D;D;D;D;D;D;.;D
Sift4G
Uncertain
0.025
D;D;D;D;D;D;D;D;.
Polyphen
1.0
D;D;D;.;D;D;D;.;.
Vest4
0.85
MutPred
0.72
Loss of ubiquitination at K345 (P = 0.0148);Loss of ubiquitination at K345 (P = 0.0148);Loss of ubiquitination at K345 (P = 0.0148);.;Loss of ubiquitination at K345 (P = 0.0148);.;Loss of ubiquitination at K345 (P = 0.0148);.;.;
MVP
0.23
MPC
1.1
ClinPred
0.95
D
GERP RS
4.7
Varity_R
0.51
gMVP
0.69

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: chr2-201334712; API