NM_003978.5(PSTPIP1):c.838+9C>T AND Pyogenic arthritis-pyoderma gangrenosum-acne syndrome

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Oct 10, 2022
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:: RCV000642407.13

Allele description [Variation Report for NM_003978.5(PSTPIP1):c.838+9C>T]

NM_003978.5(PSTPIP1):c.838+9C>T

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.838+9C>T

HGVS:

NC_000015.10:g.77032403C>T
NG_007526.1:g.42280C>T
NM_001321135.2:c.847C>T
NM_001321136.2:c.811+9C>T
NM_001321137.1:c.1033+9C>T
NM_003978.5:c.838+9C>TMANE SELECT
NP_001308064.1:p.Arg283Trp
LRG_172t1:c.838+9C>T
LRG_172:g.42280C>T
NC_000015.9:g.77324744C>T
NM_003978.3:c.838+9C>T

Protein change:

R283W

Links:

dbSNP: rs778120164

NCBI 1000 Genomes Browser:

rs778120164

Molecular consequence:

NM_001321136.2:c.811+9C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001321137.1:c.1033+9C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_003978.5:c.838+9C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001321135.2:c.847C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Pyogenic arthritis-pyoderma gangrenosum-acne syndrome
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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Chain E, Saccharomyces cerevisiae Atg19(412-415)
Chain E, Saccharomyces cerevisiae Atg19(412-415)
gi|217035309|pdb|2ZPN|E

Protein
C4orf33 chromosome 4 open reading frame 33 [Homo sapiens]
C4orf33 chromosome 4 open reading frame 33 [Homo sapiens]
Gene ID:132321

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000764081	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Oct 10, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002049925	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2021)	Likely benign (Feb 5, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000764081

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Oct 10, 2022)

germline

clinical testing

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

SCV002049925

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2021)

Likely benign
(Feb 5, 2021)

germline

clinical testing

Citation Link

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 Invitae, SCV000764081.4

#	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

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV002049925.1

#	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

Last Updated: Feb 14, 2024

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