19-17725869-C-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_018174.6(MAP1S):​c.485C>A​(p.Pro162Gln) 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. 15/21 in silico tools predict 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. P162L) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)

Consequence

MAP1S
NM_018174.6 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.395
Variant links:
Genes affected
MAP1S (HGNC:15715): (microtubule associated protein 1S) Enables DNA binding activity and cytoskeletal protein binding activity. Involved in microtubule bundle formation; neuron projection morphogenesis; and regulation of chromatin disassembly. Located in several cellular components, including microtubule cytoskeleton; nuclear lumen; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.058611423).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAP1SNM_018174.6 linkc.485C>A p.Pro162Gln missense_variant Exon 5 of 7 ENST00000324096.9 NP_060644.4 Q66K74-1
MAP1SNM_001308363.2 linkc.407C>A p.Pro136Gln missense_variant Exon 5 of 7 NP_001295292.1 Q66K74-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAP1SENST00000324096.9 linkc.485C>A p.Pro162Gln missense_variant Exon 5 of 7 1 NM_018174.6 ENSP00000325313.3 Q66K74-1

Frequencies

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.084
BayesDel_addAF
Benign
-0.28
T
BayesDel_noAF
Benign
-0.63
CADD
Benign
0.21
DANN
Benign
0.75
DEOGEN2
Benign
0.0058
T;T;.;.
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.4
FATHMM_MKL
Benign
0.0044
N
LIST_S2
Benign
0.52
T;T;T;T
M_CAP
Benign
0.0058
T
MetaRNN
Benign
0.059
T;T;T;T
MetaSVM
Benign
-0.93
T
MutationAssessor
Benign
0.20
.;N;.;.
PrimateAI
Benign
0.27
T
PROVEAN
Benign
-0.25
.;N;.;N
REVEL
Benign
0.028
Sift
Benign
0.30
.;T;.;T
Sift4G
Benign
0.40
T;T;T;T
Polyphen
0.47
.;P;.;.
Vest4
0.16, 0.14
MutPred
0.26
Loss of glycosylation at P162 (P = 0.0225);Loss of glycosylation at P162 (P = 0.0225);.;.;
MVP
0.068
MPC
0.27
ClinPred
0.16
T
GERP RS
-4.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.025
gMVP
0.29

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: chr19-17836678; API