chr2-135133944-C-A

Variant names:

• chr2-135133944-C-A
• rs267606996
• NM_012233.3:c.1410C>A

Variant summary

Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PVS1 PM2 PP5

The NM_012233.3(RAB3GAP1):​c.1410C>A​(p.Tyr470*) variant causes a stop gained 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 Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: RAB3GAP1 NM_012233.3 stop_gained
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 2.54
• Publications: 2 publications found

Genes affected

RAB3GAP1 (HGNC:17063): (RAB3 GTPase activating protein catalytic subunit 1) This gene encodes the catalytic subunit of a Rab GTPase activating protein. The encoded protein forms a heterodimer with a non-catalytic subunit to specifically regulate the activity of members of the Rab3 subfamily of small G proteins. This protein mediates the hydrolysis of GTP bound Rab3 to the GDP bound form. Mutations in this gene are associated with Warburg micro syndrome. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Feb 2010]

RAB3GAP1 Gene-Disease associations (from GenCC):

• Warburg micro syndrome

  Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
• Warburg micro syndrome 1

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
• cataract-intellectual disability-hypogonadism syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 11 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 2-135133944-C-A is Pathogenic according to our data. Variant chr2-135133944-C-A is described in CliVar as Pathogenic. Clinvar id is 7061.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr2-135133944-C-A is described in CliVar as Pathogenic. Clinvar id is 7061.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr2-135133944-C-A is described in CliVar as Pathogenic. Clinvar id is 7061.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr2-135133944-C-A is described in CliVar as Pathogenic. Clinvar id is 7061.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr2-135133944-C-A is described in CliVar as Pathogenic. Clinvar id is 7061.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr2-135133944-C-A is described in CliVar as Pathogenic. Clinvar id is 7061.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr2-135133944-C-A is described in CliVar as Pathogenic. Clinvar id is 7061.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr2-135133944-C-A is described in CliVar as Pathogenic. Clinvar id is 7061.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr2-135133944-C-A is described in CliVar as Pathogenic. Clinvar id is 7061.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr2-135133944-C-A is described in CliVar as Pathogenic. Clinvar id is 7061.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB3GAP1	NM_012233.3	c.1410C>A	p.Tyr470*	stop_gained	Exon 15 of 24	ENST00000264158.13	NP_036365.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB3GAP1	ENST00000264158.13	c.1410C>A	p.Tyr470*	stop_gained	Exon 15 of 24	1	NM_012233.3	ENSP00000264158.8

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Warburg micro syndrome 1 Pathogenic:1

Oct 01, 2010

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.62
CADD	Pathogenic	36
DANN	Uncertain	1.0
Eigen	Pathogenic	0.78
Eigen_PC	Uncertain	0.65
FATHMM_MKL	Uncertain	0.94	D
PhyloP100		2.5
Vest4		0.96
GERP RS		5.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=0/200	disease causing (ClinVar)

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

Other links and lift over

dbSNP: rs267606996; hg19: chr2-135891514;