chrX-46837089-CGGGCTGGGACCAT-C

Variant names:

• chrX-46837089-CGGGCTGGGACCAT-C
• rs2147074584
• NM_006915.3:c.-5_8delGGACCATGGGCTG

Variant summary

Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1 PS1_Moderate PP5_Moderate

The NM_006915.3(RP2):​c.-5_8delGGACCATGGGCTG​(p.Met1fs) variant causes a frameshift, start lost change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 23)
• Consequence: RP2 NM_006915.3 frameshift, start_lost
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 2.14
• Publications: 0 publications found

Genes affected

RP2 (HGNC:10274): (RP2 activator of ARL3 GTPase) The RP2 locus has been implicated as one cause of X-linked retinitis pigmentosa. The predicted gene product shows homology with human cofactor C, a protein involved in the ultimate step of beta-tubulin folding. Progressive retinal degeneration may therefore be due to the accumulation of incorrectly-folded photoreceptor or neuron-specific tubulin isoforms followed by progressive cell death [provided by RefSeq, Jul 2008]

RP2 Gene-Disease associations (from GenCC):

• retinitis pigmentosa 2

  Inheritance: XL Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), G2P
• RP2-related retinopathy

  Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
• retinitis pigmentosa

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 12 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 154 pathogenic variants in the truncated region.
• PS1: Another start lost variant in NM_006915.3 (RP2) was described as [Likely_pathogenic] in ClinVar
• PP5: Variant X-46837089-CGGGCTGGGACCAT-C is Pathogenic according to our data. Variant chrX-46837089-CGGGCTGGGACCAT-C is described in ClinVar as Pathogenic. ClinVar VariationId is 1384049.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006915.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RP2	NM_006915.3	MANE Select	c.-5_8delGGACCATGGGCTG	p.Met1fs	frameshift start_lost	Exon 1 of 5	NP_008846.2	O75695
	RP2	NM_006915.3	MANE Select	c.-5_8delGGACCATGGGCTG		5_prime_UTR	Exon 1 of 5	NP_008846.2	O75695

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RP2	ENST00000218340.4	TSL:1 MANE Select	c.-5_8delGGACCATGGGCTG	p.Met1fs	frameshift start_lost	Exon 1 of 5	ENSP00000218340.3	O75695
	RP2	ENST00000218340.4	TSL:1 MANE Select	c.-5_8delGGACCATGGGCTG		5_prime_UTR	Exon 1 of 5	ENSP00000218340.3	O75695
	RP2	ENST00000891112.1		c.-5_8delGGACCATGGGCTG	p.Met1fs	frameshift start_lost	Exon 1 of 6	ENSP00000561171.1

Frequencies

GnomAD3 genomes Cov.: 23

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 23

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
1	-	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2147074584; hg19: chrX-46696524;