NM_001032291.3:c.616A>G

Variant summary

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

The NM_001032291.3(PSRC1):​c.616A>G​(p.Ser206Gly) 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. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

PSRC1
NM_001032291.3 missense

Scores

19

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.0690
Variant links:
Genes affected
PSRC1 (HGNC:24472): (proline and serine rich coiled-coil 1) This gene encodes a proline-rich protein that is a target for regulation by the tumor suppressor protein p53. The encoded protein plays an important role in mitosis by recruiting and regulating microtubule depolymerases that destabalize microtubules. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Apr 2014]

Genome browser will be placed here

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=0.063551694).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PSRC1NM_001032291.3 linkc.616A>G p.Ser206Gly missense_variant Exon 5 of 8 ENST00000369909.7 NP_001027462.1 Q6PGN9-2A0A024R099A8K0M8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PSRC1ENST00000369909.7 linkc.616A>G p.Ser206Gly missense_variant Exon 5 of 8 1 NM_001032291.3 ENSP00000358925.2 Q6PGN9-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
33
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
Dec 22, 2023
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.616A>G (p.S206G) alteration is located in exon 5 (coding exon 4) of the PSRC1 gene. This alteration results from a A to G substitution at nucleotide position 616, causing the serine (S) at amino acid position 206 to be replaced by a glycine (G). 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
Benign
0.068
BayesDel_addAF
Benign
-0.21
T
BayesDel_noAF
Benign
-0.54
CADD
Benign
8.5
DANN
Benign
0.96
DEOGEN2
Benign
0.054
.;.;.;.;T;.;T
Eigen
Benign
-0.86
Eigen_PC
Benign
-0.75
FATHMM_MKL
Benign
0.10
N
LIST_S2
Benign
0.56
T;.;.;T;T;.;T
M_CAP
Benign
0.0048
T
MetaRNN
Benign
0.064
T;T;T;T;T;T;T
MetaSVM
Benign
-0.97
T
MutationAssessor
Benign
0.46
N;N;N;N;N;N;.
PrimateAI
Benign
0.31
T
PROVEAN
Benign
-1.9
N;N;N;N;.;N;N
REVEL
Benign
0.038
Sift
Benign
0.20
T;T;T;T;.;T;T
Sift4G
Benign
0.39
T;T;T;T;T;T;.
Polyphen
0.0010
B;B;B;B;B;B;.
Vest4
0.22
MutPred
0.27
Loss of glycosylation at S206 (P = 0.003);Loss of glycosylation at S206 (P = 0.003);Loss of glycosylation at S206 (P = 0.003);Loss of glycosylation at S206 (P = 0.003);Loss of glycosylation at S206 (P = 0.003);Loss of glycosylation at S206 (P = 0.003);Loss of glycosylation at S206 (P = 0.003);
MVP
0.45
MPC
0.16
ClinPred
0.065
T
GERP RS
-0.65
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.033
gMVP
0.059

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

LitVar

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

Other links and lift over

dbSNP: rs1657032167; hg19: chr1-109823777; API