5-131430969-T-G

Variant summary

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

The NM_016340.6(RAPGEF6):​c.4355A>C​(p.Gln1452Pro) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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. Q1452R) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 31)

Consequence

RAPGEF6
NM_016340.6 missense

Scores

6
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.83
Variant links:
Genes affected
RAPGEF6 (HGNC:20655): (Rap guanine nucleotide exchange factor 6) Enables several functions, including GTP-dependent protein binding activity; guanyl-nucleotide exchange factor activity; and phosphatidic acid binding activity. Involved in microvillus assembly; positive regulation of GTPase activity; and protein localization to plasma membrane. Located in several cellular components, including apical plasma membrane; centrosome; and endocytic vesicle. [provided by Alliance of Genome Resources, Apr 2022]

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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=0.1581457).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RAPGEF6NM_016340.6 linkc.4355A>C p.Gln1452Pro missense_variant 26/28 ENST00000509018.6 NP_057424.3 Q8TEU7-1
RAPGEF6NM_001164386.2 linkc.4379A>C p.Gln1460Pro missense_variant 27/29 NP_001157858.1 Q8TEU7-4B2RTU6
RAPGEF6NM_001164387.2 linkc.4394A>C p.Gln1465Pro missense_variant 28/29 NP_001157859.1 Q8TEU7-3
RAPGEF6NM_001164388.2 linkc.4379A>C p.Gln1460Pro missense_variant 27/28 NP_001157860.1 Q8TEU7-5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RAPGEF6ENST00000509018.6 linkc.4355A>C p.Gln1452Pro missense_variant 26/281 NM_016340.6 ENSP00000421684.1 Q8TEU7-1
ENSG00000273217ENST00000514667.1 linkc.4505A>C p.Gln1502Pro missense_variant 27/292 ENSP00000426948.1 E9PCH4

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
66
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.14
T
BayesDel_noAF
Benign
-0.44
CADD
Uncertain
23
DANN
Uncertain
0.99
DEOGEN2
Benign
0.13
T;.;.;.;.
Eigen
Benign
-0.32
Eigen_PC
Benign
-0.097
FATHMM_MKL
Uncertain
0.93
D
LIST_S2
Uncertain
0.86
D;D;T;D;T
M_CAP
Benign
0.0096
T
MetaRNN
Benign
0.16
T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.0
N;.;.;.;.
PrimateAI
Uncertain
0.63
T
PROVEAN
Benign
-1.3
N;.;N;.;N
REVEL
Benign
0.095
Sift
Uncertain
0.0010
D;.;D;.;D
Sift4G
Uncertain
0.047
D;D;D;D;D
Polyphen
0.0020
B;B;.;.;.
Vest4
0.26
MutPred
0.30
.;.;.;.;Loss of sheet (P = 0.0315);
MVP
0.22
MPC
0.20, 0.20
ClinPred
0.60
D
GERP RS
5.2
Varity_R
0.34
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

LitVar

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

Other links and lift over

dbSNP: rs1291602; hg19: chr5-130766662; API