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GeneBe

3-57860714-A-T

Variant summary

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

The NM_001377540.1(SLMAP):c.703A>T(p.Ser235Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000192 in 1,564,232 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S235G) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

SLMAP
NM_001377540.1 missense

Scores

7
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.67
Variant links:
Genes affected
SLMAP (HGNC:16643): (sarcolemma associated protein) This gene encodes a component of a conserved striatin-interacting phosphatase and kinase complex. Striatin family complexes participate in a variety of cellular processes including signaling, cell cycle control, cell migration, Golgi assembly, and apoptosis. The protein encoded by this gene is a coiled-coil, tail-anchored membrane protein with a single C-terminal transmembrane domain that is posttranslationally inserted into membranes. Mutations in this gene are associated with Brugada syndrome, a cardiac channelopathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]

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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=0.15676326).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLMAPNM_001377540.1 linkuse as main transcriptc.703A>T p.Ser235Cys missense_variant 9/25 ENST00000671191.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLMAPENST00000671191.1 linkuse as main transcriptc.703A>T p.Ser235Cys missense_variant 9/25 NM_001377540.1 P4

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152180
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000142
AC:
2
AN:
1412052
Hom.:
0
Cov.:
29
AF XY:
0.00000142
AC XY:
1
AN XY:
701794
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000183
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152180
Hom.:
0
Cov.:
32
AF XY:
0.0000134
AC XY:
1
AN XY:
74360
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.069
T
BayesDel_noAF
Benign
-0.34
Cadd
Uncertain
24
Dann
Uncertain
0.99
Eigen
Uncertain
0.26
Eigen_PC
Uncertain
0.27
FATHMM_MKL
Uncertain
0.89
D
M_CAP
Benign
0.018
T
MetaRNN
Benign
0.16
T;T;T;T;T
MetaSVM
Benign
-0.93
T
MutationAssessor
Benign
0.77
N;N;N;N;N
MutationTaster
Benign
0.98
D;D;D;D;D;D
PrimateAI
Uncertain
0.62
T
PROVEAN
Uncertain
-2.8
D;D;D;D;D
REVEL
Benign
0.18
Sift
Benign
0.030
D;D;D;D;D
Sift4G
Uncertain
0.023
D;D;D;D;D
Polyphen
1.0
D;D;D;D;D
Vest4
0.20
MutPred
0.25
Gain of catalytic residue at L236 (P = 0.0107);Gain of catalytic residue at L236 (P = 0.0107);Gain of catalytic residue at L236 (P = 0.0107);Gain of catalytic residue at L236 (P = 0.0107);Gain of catalytic residue at L236 (P = 0.0107);
MVP
0.33
MPC
0.19
ClinPred
0.64
D
GERP RS
2.9
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.19
gMVP
0.18

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs774215191; hg19: chr3-57846441; API