NM_002764.4:c.641G>C

Variant names:

• chrX-107645287-G-C
• rs867288458
• NM_002764.4:c.641G>C

Variant summary

Our verdict is Likely pathogenic. The variant received 7 ACMG points: 7P and 0B. PM2 PM5 PP3_Moderate PP5

The NM_002764.4(PRPS1):​c.641G>C​(p.Arg214Pro) variant causes a missense change. 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 Likely pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R214Q) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 23)
• Consequence: PRPS1 NM_002764.4 missense
• Clinical Significance: Likely pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 6.50
• Publications: 5 publications found

Genes affected

PRPS1 (HGNC:9462): (phosphoribosyl pyrophosphate synthetase 1) This gene encodes an enzyme that catalyzes the phosphoribosylation of ribose 5-phosphate to 5-phosphoribosyl-1-pyrophosphate, which is necessary for purine metabolism and nucleotide biosynthesis. Defects in this gene are a cause of phosphoribosylpyrophosphate synthetase superactivity, Charcot-Marie-Tooth disease X-linked recessive type 5 and Arts Syndrome. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2011]

PRPS1 Gene-Disease associations (from GenCC):

• Arts syndrome

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae), PanelApp Australia
• Charcot-Marie-Tooth disease X-linked recessive 5

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: PanelApp Australia, Orphanet, G2P
• hearing loss, X-linked 1

  Inheritance: XL Classification: DEFINITIVE, STRONG Submitted by: G2P, PanelApp Australia
• phosphoribosylpyrophosphate synthetase superactivity

  Inheritance: XL Classification: DEFINITIVE, STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P, ClinGen
• PRPS1 deficiency disorder

  Inheritance: XL Classification: DEFINITIVE Submitted by: Illumina, ClinGen
• mild phosphoribosylpyrophosphate synthetase superactivity

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
• severe phosphoribosylpyrophosphate synthetase superactivity

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
• X-linked intellectual disability-limb spasticity-retinal dystrophy-diabetes insipidus syndrome

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
• X-linked nonsyndromic hearing loss

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000289923 (HGNC:):

ACMG classification

Our verdict: Likely_pathogenic. The variant received 7 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chrX-107645286-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 446163.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.864
• PP5: Variant X-107645287-G-C is Pathogenic according to our data. Variant chrX-107645287-G-C is described in CliVar as Likely_pathogenic. Clinvar id is 446164.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-107645287-G-C is described in CliVar as Likely_pathogenic. Clinvar id is 446164.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-107645287-G-C is described in CliVar as Likely_pathogenic. Clinvar id is 446164.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-107645287-G-C is described in CliVar as Likely_pathogenic. Clinvar id is 446164.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-107645287-G-C is described in CliVar as Likely_pathogenic. Clinvar id is 446164.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-107645287-G-C is described in CliVar as Likely_pathogenic. Clinvar id is 446164.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-107645287-G-C is described in CliVar as Likely_pathogenic. Clinvar id is 446164.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-107645287-G-C is described in CliVar as Likely_pathogenic. Clinvar id is 446164.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-107645287-G-C is described in CliVar as Likely_pathogenic. Clinvar id is 446164.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRPS1	NM_002764.4	c.641G>C	p.Arg214Pro	missense_variant	Exon 5 of 7	ENST00000372435.10	NP_002755.1
PRPS1	NM_001204402.2	c.29G>C	p.Arg10Pro	missense_variant	Exon 2 of 4		NP_001191331.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRPS1	ENST00000372435.10	c.641G>C	p.Arg214Pro	missense_variant	Exon 5 of 7	1	NM_002764.4	ENSP00000361512.4

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 23

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Retinal dystrophy;C3887873:Hearing loss Pathogenic:1

Jan 01, 2017

Hardcastle Lab, UCL Institute of Ophthalmology

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: research

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.59	D
BayesDel_noAF	Pathogenic	0.61
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Pathogenic	0.88	D;D;.;.
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.88	D;D;D;D
M_CAP	Uncertain	0.23	D
MetaRNN	Pathogenic	0.86	D;D;D;D
MetaSVM	Uncertain	0.72	D
MutationAssessor	Pathogenic	3.5	.;H;.;.
PhyloP100		6.5
PrimateAI	Pathogenic	0.87	D
PROVEAN	Uncertain	-4.2	.;D;.;.
REVEL	Pathogenic	0.75
Sift	Uncertain	0.0010	.;D;.;.
Sift4G	Uncertain	0.014	D;D;.;.
Polyphen		0.12	.;B;.;.
Vest4		0.81
MutPred		0.66		.;Gain of methylation at K212 (P = 0.0605);Gain of methylation at K212 (P = 0.0605);.;
MVP		1.0
MPC		2.3
ClinPred		0.99	D
GERP RS		4.7
PromoterAI		0.017	Neutral
Varity_R		0.98
gMVP		1.0
Mutation Taster		=2/98	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: rs867288458; hg19: chrX-106888517;