rs760241426
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_012414.4(RAB3GAP2):c.3183C>T(p.Phe1061Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000692 in 1,444,166 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.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
RAB3GAP2
NM_012414.4 synonymous
NM_012414.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.26
Publications
0 publications found
Genes affected
RAB3GAP2 (HGNC:17168): (RAB3 GTPase activating non-catalytic protein subunit 2) The protein encoded by this gene belongs to the RAB3 protein family, members of which are involved in regulated exocytosis of neurotransmitters and hormones. This protein forms the Rab3 GTPase-activating complex with RAB3GAP1, where it constitutes the regulatory subunit, whereas the latter functions as the catalytic subunit. This gene has the highest level of expression in the brain, consistent with it having a key role in neurodevelopment. Mutations in this gene are associated with Martsolf syndrome.[provided by RefSeq, Oct 2009]
RAB3GAP2 Gene-Disease associations (from GenCC):
- Martsolf syndrome 1Inheritance: AR Classification: DEFINITIVE Submitted by: G2P
- RAB18 deficiencyInheritance: AR Classification: DEFINITIVE Submitted by: Ambry Genetics
- Warburg micro syndromeInheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
- Warburg micro syndrome 2Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- autosomal recessive spastic paraplegia type 69Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- cataract-intellectual disability-hypogonadism syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.31).
BP7
Synonymous conserved (PhyloP=3.26 with no splicing effect.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.92e-7 AC: 1AN: 1444166Hom.: 0 Cov.: 29 AF XY: 0.00000139 AC XY: 1AN XY: 719512 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1444166
Hom.:
Cov.:
29
AF XY:
AC XY:
1
AN XY:
719512
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33028
American (AMR)
AF:
AC:
0
AN:
44680
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26014
East Asian (EAS)
AF:
AC:
0
AN:
39422
South Asian (SAS)
AF:
AC:
0
AN:
85858
European-Finnish (FIN)
AF:
AC:
0
AN:
53394
Middle Eastern (MID)
AF:
AC:
0
AN:
5732
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1096210
Other (OTH)
AF:
AC:
0
AN:
59828
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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