Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_003978.5(PSTPIP1):c.915C>T(p.Cys305Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.023 in 1,602,812 control chromosomes in the GnomAD database, including 817 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.041 ( 221 hom., cov: 33)

Exomes 𝑓: 0.021 ( 596 hom. )

Consequence

PSTPIP1
NM_003978.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -2.94

Publications

9 publications found

Variant links:

Genes affected

PSTPIP1 (HGNC:9580): (proline-serine-threonine phosphatase interacting protein 1) This gene encodes a cytoskeletal protein that is highly expressed in hemopoietic tissues. This protein functions via its interaction with several different proteins involved in cytoskeletal organization and inflammatory processes. It binds to the cytoplasmic tail of CD2, an effector of T cell activation and adhesion, downregulating CD2-triggered adhesion. It binds PEST-type protein tyrosine phosphatases (PTP) and directs them to c-Abl kinase to mediate c-Abl dephosphorylation, thereby, regulating c-Abl activity. It also interacts with pyrin, which is found in association with the cytoskeleton in myeloid/monocytic cells and modulates immunoregulatory functions. Mutations in this gene are associated with PAPA (pyogenic sterile arthritis, pyoderma gangrenosum, and acne) syndrome. It is hypothesized that the disease-causing mutations compromise physiologic signaling necessary for the maintenance of a proper inflammatory response. [provided by RefSeq, Mar 2016]

PSTPIP1 Gene-Disease associations (from GenCC):

pyogenic arthritis-pyoderma gangrenosum-acne syndrome
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae)
autoinflammatory syndrome
Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
recurrent infections-inflammatory syndrome due to zinc metabolism disorder syndrome
Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

PSTPIP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 15-77032938-C-T is Benign according to our data. Variant chr15-77032938-C-T is described in ClinVar as Benign. ClinVar VariationId is 259212.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.94 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.093 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003978.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
PSTPIP1	NM_003978.5	MANE Select	c.915C>T	p.Cys305Cys	synonymous	Exon 12 of 15	NP_003969.2
PSTPIP1	NM_001321137.1		c.1110C>T	p.Cys370Cys	synonymous	Exon 13 of 16	NP_001308066.1
PSTPIP1	NM_001411086.1		c.915C>T	p.Cys305Cys	synonymous	Exon 12 of 15	NP_001398015.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
PSTPIP1	ENST00000558012.6	TSL:1 MANE Select	c.915C>T	p.Cys305Cys	synonymous	Exon 12 of 15	ENSP00000452746.1
PSTPIP1	ENST00000559785.5	TSL:1	n.1144C>T		non_coding_transcript_exon	Exon 13 of 16	ENSP00000452986.1
PSTPIP1	ENST00000560223.5	TSL:1	n.*1017C>T		non_coding_transcript_exon	Exon 13 of 16	ENSP00000454118.1

Frequencies

GnomAD3 genomes

AF:

0.0407

AC:

6199

AN:

152134

Hom.:

221

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0954

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.0158

Gnomad ASJ

AF:

0.0207

Gnomad EAS

AF:

0.0633

Gnomad SAS

AF:

0.0371

Gnomad FIN

AF:

0.0288

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0150

Gnomad OTH

AF:

0.0378

GnomAD2 exomes

AF:

0.0280

AC:

6408

AN:

228940

AF XY:

0.0272

show subpopulations

Gnomad AFR exome

AF:

0.102

Gnomad AMR exome

AF:

0.0127

Gnomad ASJ exome

AF:

0.0160

Gnomad EAS exome

AF:

0.0632

Gnomad FIN exome

AF:

0.0301

Gnomad NFE exome

AF:

0.0154

Gnomad OTH exome

AF:

0.0245

GnomAD4 exome

AF:

0.0211

AC:

30630

AN:

1450560

Hom.:

596

Cov.:

AF XY:

0.0213

AC XY:

15380

AN XY:

720466

show subpopulations

African (AFR)

AF:

0.0929

AC:

3093

AN:

33298

American (AMR)

AF:

0.0133

AC:

580

AN:

43592

Ashkenazi Jewish (ASJ)

AF:

0.0169

AC:

436

AN:

25782

East Asian (EAS)

AF:

0.0701

AC:

2761

AN:

39380

South Asian (SAS)

AF:

0.0380

AC:

3207

AN:

84402

European-Finnish (FIN)

AF:

0.0309

AC:

1584

AN:

51316

Middle Eastern (MID)

AF:

0.0188

AC:

108

AN:

5752

European-Non Finnish (NFE)

AF:

0.0156

AC:

17222

AN:

1107118

Other (OTH)

AF:

0.0274

AC:

1639

AN:

59920

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

1482

2964

4445

5927

7409

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

768

1536

2304

3072

3840

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0408

AC:

6211

AN:

152252

Hom.:

221

Cov.:

AF XY:

0.0408

AC XY:

3038

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.0955

AC:

3968

AN:

41540

American (AMR)

AF:

0.0158

AC:

241

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0207

AC:

AN:

3470

East Asian (EAS)

AF:

0.0634

AC:

328

AN:

5170

South Asian (SAS)

AF:

0.0369

AC:

178

AN:

4828

European-Finnish (FIN)

AF:

0.0288

AC:

306

AN:

10620

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0149

AC:

1015

AN:

68004

Other (OTH)

AF:

0.0369

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

314

628

942

1256

1570

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

222

296

370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0280

Hom.:

243

Bravo

AF:

0.0421

Asia WGS

AF:

0.0640

AC:

223

AN:

3478

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

Pyogenic arthritis-pyoderma gangrenosum-acne syndrome (3)

not provided (2)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_noAF

Benign

-0.79

CADD

Benign

2.5

(source)

DANN

Benign

0.55

PhyloP100

-2.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

rs11858480

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

ClinVar submissions as Germline

Computational scores

Splicing

Publications

Other links and lift over