NM_003978.5(PSTPIP1):c.929+18G>A AND Pyogenic arthritis-pyoderma gangrenosum-acne syndrome

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jan 4, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001001289.11

Allele description [Variation Report for NM_003978.5(PSTPIP1):c.929+18G>A]

NM_003978.5(PSTPIP1):c.929+18G>A

Gene:

PSTPIP1:proline-serine-threonine phosphatase interacting protein 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q24.3

Genomic location:

Preferred name:

NM_003978.5(PSTPIP1):c.929+18G>A

HGVS:

NC_000015.10:g.77032970G>A
NG_007526.1:g.42847G>A
NM_001321135.2:c.872+542G>A
NM_001321136.2:c.902+18G>A
NM_001321137.1:c.1124+18G>A
NM_003978.5:c.929+18G>AMANE SELECT
LRG_172:g.42847G>A
NC_000015.9:g.77325311G>A

Links:

dbSNP: rs773172907

NCBI 1000 Genomes Browser:

rs773172907

Molecular consequence:

NM_001321135.2:c.872+542G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001321136.2:c.902+18G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001321137.1:c.1124+18G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_003978.5:c.929+18G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Pyogenic arthritis-pyoderma gangrenosum-acne syndrome (PAPA)
Synonyms:: Pyogenic arthritis, pyoderma gangrenosum and acne; Pyogenic arthritis, pyoderma gangrenosum, and severe cystic acne; Familial recurrent arthritis
Identifiers:: MONDO: MONDO:0011462; MedGen: C1858361; Orphanet: 69126; OMIM: 604416

Recent activity

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cytochrome oxidase subunit 1, partial (mitochondrion) [Phosichthys argenteus]
cytochrome oxidase subunit 1, partial (mitochondrion) [Phosichthys argenteus]
gi|343223971|gb|AEM15227.1|

Protein
cardiac muscle myosin heavy chain 6 alpha protein, partial [Phosichthys argenteu...
cardiac muscle myosin heavy chain 6 alpha protein, partial [Phosichthys argenteus]
gi|321152121|gb|ADW66420.1|

Protein
glucocorticoid receptor, partial [Lamprotornis caudatus]
glucocorticoid receptor, partial [Lamprotornis caudatus]
gi|1031914713|gb|ANG55556.1|

Protein
interleukin-11 receptor subunit alpha-1 precursor [Mus musculus]
interleukin-11 receptor subunit alpha-1 precursor [Mus musculus]
gi|7110651|ref|NP_034679.1|

Protein
Loss of Purkinje cells in the cerebellar vermis
Loss of Purkinje cells in the cerebellar vermis

MedGen

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001158468	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Likely benign (Dec 14, 2019)	germline	clinical testing	Citation Link,
SCV004554049	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 4, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001158468

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)

Likely benign
(Dec 14, 2019)

germline

clinical testing

Citation Link,

SCV004554049

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 4, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV001158468.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004554049.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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