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GeneBe

1-70250757-A-T

Variant summary

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

The NM_001350605.2(SRSF11):c.1407A>T(p.Lys469Asn) 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. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

SRSF11
NM_001350605.2 missense

Scores

1
7
9

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.55
Variant links:
Genes affected
SRSF11 (HGNC:10782): (serine and arginine rich splicing factor 11) This gene encodes 54-kD nuclear protein that contains an arginine/serine-rich region similar to segments found in pre-mRNA splicing factors. Although the function of this protein is not yet known, structure and immunolocalization data suggest that it may play a role in pre-mRNA processing. Alternative splicing results in multiple transcript variants encoding different proteins. In addition, a pseudogene of this gene has been found on chromosome 12.[provided by RefSeq, Sep 2010]

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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=0.20188224).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SRSF11NM_001350605.2 linkuse as main transcriptc.1407A>T p.Lys469Asn missense_variant 12/12 ENST00000370949.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SRSF11ENST00000370949.2 linkuse as main transcriptc.1407A>T p.Lys469Asn missense_variant 12/121 NM_001350605.2 P4Q05519-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

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

Submissions by phenotype

SRSF11-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesDec 13, 2023The SRSF11 c.1404A>T variant is predicted to result in the amino acid substitution p.Lys468Asn. To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.66
BayesDel_addAF
Benign
-0.15
T
BayesDel_noAF
Benign
-0.46
CADD
Uncertain
24
DANN
Uncertain
1.0
Eigen
Uncertain
0.29
Eigen_PC
Uncertain
0.23
FATHMM_MKL
Uncertain
0.88
D
LIST_S2
Uncertain
0.93
D;D;D
M_CAP
Benign
0.031
D
MetaRNN
Benign
0.20
T;T;T
MetaSVM
Benign
-0.83
T
MutationTaster
Benign
1.0
D;D;D;D
PrimateAI
Uncertain
0.68
T
PROVEAN
Benign
-0.63
N;N;N
REVEL
Benign
0.11
Sift
Uncertain
0.0060
D;D;D
Sift4G
Benign
0.075
T;T;T
Polyphen
0.99, 1.0
.;D;D
Vest4
0.40
MutPred
0.24
.;Loss of ubiquitination at K469 (P = 0.003);.;
MVP
0.34
MPC
2.1
ClinPred
0.72
D
GERP RS
1.8
RBP_binding_hub_radar
1.1
RBP_regulation_power_radar
2.8
Varity_R
0.25
gMVP
0.12

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: chr1-70716440; API