chr14-64972063-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_001308154.2(RAB15):​c.14A>G​(p.Tyr5Cys) 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 pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 31)

Consequence

RAB15
NM_001308154.2 missense

Scores

8
6
5

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.50
Variant links:
Genes affected
RAB15 (HGNC:20150): (RAB15, member RAS oncogene family) Predicted to enable GTP binding activity and GTPase activity. Involved in positive regulation of regulated secretory pathway. Located in cilium; endosome membrane; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.786

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RAB15NM_001308154.2 linkuse as main transcriptc.14A>G p.Tyr5Cys missense_variant 1/7 ENST00000533601.7 NP_001295083.1
CHURC1-FNTBNM_001202559.1 linkuse as main transcriptc.328-32186T>C intron_variant NP_001189488.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RAB15ENST00000533601.7 linkuse as main transcriptc.14A>G p.Tyr5Cys missense_variant 1/71 NM_001308154.2 ENSP00000434103 P1P59190-1

Frequencies

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

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMay 28, 2024The c.14A>G (p.Y5C) alteration is located in exon 1 (coding exon 1) of the RAB15 gene. This alteration results from a A to G substitution at nucleotide position 14, causing the tyrosine (Y) at amino acid position 5 to be replaced by a cysteine (C). 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
Pathogenic
0.91
BayesDel_addAF
Uncertain
0.093
D
BayesDel_noAF
Benign
-0.10
CADD
Pathogenic
29
DANN
Uncertain
0.99
DEOGEN2
Benign
0.12
.;T;.;.
Eigen
Uncertain
0.27
Eigen_PC
Benign
0.19
FATHMM_MKL
Benign
0.71
D
LIST_S2
Pathogenic
0.99
D;D;D;D
M_CAP
Pathogenic
0.94
D
MetaRNN
Pathogenic
0.79
D;D;D;D
MetaSVM
Uncertain
-0.13
T
MutationAssessor
Uncertain
2.0
M;M;.;.
MutationTaster
Benign
1.0
D;D;N;N
PrimateAI
Pathogenic
0.92
D
PROVEAN
Pathogenic
-7.7
D;D;.;.
REVEL
Uncertain
0.58
Sift
Pathogenic
0.0
D;D;.;.
Sift4G
Pathogenic
0.0
D;D;.;.
Polyphen
1.0
D;.;.;.
Vest4
0.24
MutPred
0.56
Loss of ubiquitination at V3 (P = 0.0472);Loss of ubiquitination at V3 (P = 0.0472);.;.;
MVP
0.94
MPC
1.9
ClinPred
1.0
D
GERP RS
2.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.6
Varity_R
0.76
gMVP
0.82

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: chr14-65438781; API