NM_001611.5(ACP5):c.919A>T (p.Ile307Phe) AND Spondyloenchondrodysplasia with immune dysregulation

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 11, 2020
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001318436.5

Allele description

NM_001611.5(ACP5):c.919A>T (p.Ile307Phe)

Gene:

ACP5:acid phosphatase 5, tartrate resistant [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.2

Genomic location:

Preferred name:

NM_001611.5(ACP5):c.919A>T (p.Ile307Phe)

HGVS:

NC_000019.10:g.11575069T>A
NG_028127.1:g.8918A>T
NM_001111034.3:c.919A>T
NM_001111035.3:c.919A>T
NM_001111036.3:c.919A>T
NM_001322023.2:c.919A>T
NM_001611.5:c.919A>TMANE SELECT
NP_001104504.1:p.Ile307Phe
NP_001104505.1:p.Ile307Phe
NP_001104506.1:p.Ile307Phe
NP_001308952.1:p.Ile307Phe
NP_001602.1:p.Ile307Phe
LRG_1218t1:c.919A>T
LRG_1218:g.8918A>T
LRG_1218p1:p.Ile307Phe
NC_000019.9:g.11685884T>A

Protein change:

I307F

Links:

dbSNP: rs1483232010

NCBI 1000 Genomes Browser:

rs1483232010

Molecular consequence:

NM_001111034.3:c.919A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001111035.3:c.919A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001111036.3:c.919A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322023.2:c.919A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001611.5:c.919A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Spondyloenchondrodysplasia with immune dysregulation (SPENCDI)
Synonyms:: COMBINED IMMUNODEFICIENCY WITH AUTOIMMUNITY AND SPONDYLOMETAPHYSEAL DYSPLASIA; ROIFMAN IMMUNOSKELETAL SYNDROME; SPONDYLOENCHONDRODYSPLASIA WITH OR WITHOUT IMMUNE DYSREGULATION
Identifiers:: MONDO: MONDO:0011939; MedGen: C1842763; OMIM: 607944

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001509135	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 11, 2020)	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

SCV001509135

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 11, 2020)

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 Invitae, SCV001509135.3

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Not Available"). This variant has not been reported in the literature in individuals with ACP5-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces isoleucine with phenylalanine at codon 307 of the ACP5 protein (p.Ile307Phe). The isoleucine residue is weakly conserved and there is a small physicochemical difference between isoleucine and phenylalanine.

#	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 28, 2024

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