GeneBe

rs55909412

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_003978.5(PSTPIP1):​c.-413_-402delCCTGCCTGCCTG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000981 in 1,018,872 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 28)
Exomes 𝑓: 9.8e-7 ( 0 hom. )

Consequence

PSTPIP1
NM_003978.5 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.81

Publications

0 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: Orphanet, G2P, 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

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PSTPIP1
NM_003978.5
MANE Select
c.-413_-402delCCTGCCTGCCTG
5_prime_UTR
Exon 1 of 15NP_003969.2
PSTPIP1
NM_001411086.1
c.-413_-402delCCTGCCTGCCTG
5_prime_UTR
Exon 1 of 15NP_001398015.1J3KPG6
PSTPIP1
NM_001321136.2
c.-659_-648delCCTGCCTGCCTG
5_prime_UTR
Exon 1 of 16NP_001308065.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PSTPIP1
ENST00000558012.6
TSL:1 MANE Select
c.-413_-402delCCTGCCTGCCTG
5_prime_UTR
Exon 1 of 15ENSP00000452746.1O43586-1
PSTPIP1
ENST00000559795.5
TSL:1
n.36_47delCCTGCCTGCCTG
non_coding_transcript_exon
Exon 1 of 4
PSTPIP1
ENST00000560223.5
TSL:1
n.-413_-402delCCTGCCTGCCTG
non_coding_transcript_exon
Exon 1 of 16ENSP00000454118.1H0YNR2

Frequencies

GnomAD3 genomes
Cov.:
28
GnomAD4 exome
AF:
9.81e-7
AC:
1
AN:
1018872
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
486202
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
21066
American (AMR)
AF:
0.00
AC:
0
AN:
9720
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
9444
East Asian (EAS)
AF:
0.00
AC:
0
AN:
11952
South Asian (SAS)
AF:
0.00
AC:
0
AN:
53714
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
8566
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2288
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
865754
Other (OTH)
AF:
0.0000275
AC:
1
AN:
36368
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.8

Splicing

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

Publications

Other links and lift over

dbSNP: rs55909412; hg19: chr15-77287490; API