NM_171998.4:c.574G>A

Variant names:

• chrX-155260871-C-T
• rs864309527
• NM_171998.4:c.574G>A

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2 PP3 PP5_Moderate

The NM_171998.4(RAB39B):​c.574G>A​(p.Gly192Arg) variant causes a missense change involving the alteration of a 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 (★).

• Frequency: Genomes: not found (cov: 23)
• Consequence: RAB39B NM_171998.4 missense
• Clinical Significance: Pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 7.50

Genes affected

RAB39B (HGNC:16499): (RAB39B, member RAS oncogene family) This gene encodes a member of the Rab family of proteins. Rab proteins are small GTPases that are involved in vesicular trafficking. Mutations in this gene are associated with X-linked cognitive disability. [provided by RefSeq, Aug 2013]

ACMG classification

Verdict is Uncertain_significance. Variant got 5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.808
• PP5: Variant X-155260871-C-T is Pathogenic according to our data. Variant chrX-155260871-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 218362.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-155260871-C-T is described in Lovd as [Pathogenic]. Variant chrX-155260871-C-T is described in Lovd as [Pathogenic]. Variant chrX-155260871-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB39B	NM_171998.4	c.574G>A	p.Gly192Arg	missense_variant	Exon 2 of 2	ENST00000369454.4	NP_741995.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB39B	ENST00000369454.4	c.574G>A	p.Gly192Arg	missense_variant	Exon 2 of 2	1	NM_171998.4	ENSP00000358466.3

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 23

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, single submitter

Submissions by phenotype

Parkinson disease, X-linked dominant Pathogenic:1

Sep 14, 2015

Zabetian_UW Neurogenetics Lab, University of Washington/VAPSHCS

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

It segregates with disease in the family, affects a highly conserved amino acid, and functional work whos that this mutation alters the intracellular localization of the protein. -

Early-onset parkinsonism-intellectual disability syndrome Pathogenic:1

Sep 24, 2015

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.96
BayesDel_addAF	Pathogenic	0.45	D
BayesDel_noAF	Pathogenic	0.41
CADD	Pathogenic	27
DANN	Pathogenic	1.0
DEOGEN2	Benign	0.15	T
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Uncertain	0.95	D
M_CAP	Pathogenic	0.30	D
MetaRNN	Pathogenic	0.81	D
MetaSVM	Uncertain	0.016	D
MutationAssessor	Uncertain	2.2	M
PrimateAI	Pathogenic	0.92	D
PROVEAN	Pathogenic	-5.5	D
REVEL	Pathogenic	0.79
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.0020	D
Polyphen		1.0	D
Vest4		0.62
MutPred		0.54		Gain of MoRF binding (P = 0.0607);
MVP		0.97
MPC		2.6
ClinPred		1.0	D
GERP RS		5.2
Varity_R		0.95
gMVP		0.96

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

Other links and lift over

dbSNP: rs864309527; hg19: chrX-154490156;