NM_172245.4(CSF2RA):c.689C>T (p.Thr230Met) AND Surfactant metabolism dysfunction, pulmonary, 4

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 1, 2022
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:: RCV003106190.5

Allele description [Variation Report for NM_172245.4(CSF2RA):c.689C>T (p.Thr230Met)]

NM_172245.4(CSF2RA):c.689C>T (p.Thr230Met)

Gene:

CSF2RA:colony stimulating factor 2 receptor subunit alpha [Gene - OMIM - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp22.33

Genomic location:

Preferred name:

NM_172245.4(CSF2RA):c.689C>T (p.Thr230Met)

HGVS:

NC_000023.11:g.1294370C>T
NC_000024.10:g.1294370C>T
NG_012280.1:g.30571C>T
NM_001161529.2:c.689C>T
NM_001161530.2:c.689C>T
NM_001161531.2:c.689C>T
NM_001161532.2:c.290C>T
NM_001379153.1:c.689C>T
NM_001379154.1:c.689C>T
NM_001379155.1:c.689C>T
NM_001379156.1:c.689C>T
NM_001379158.1:c.689C>T
NM_001379159.1:c.689C>T
NM_001379160.1:c.689C>T
NM_001379161.1:c.689C>T
NM_001379162.1:c.689C>T
NM_001379163.1:c.689C>T
NM_001379164.1:c.689C>T
NM_001379165.1:c.689C>T
NM_001379166.1:c.670C>T
NM_001379167.1:c.689C>T
NM_001379168.1:c.689C>T
NM_001379169.1:c.689C>T
NM_006140.6:c.689C>T
NM_172245.4:c.689C>TMANE SELECT
NM_172246.4:c.689C>T
NM_172247.3:c.689C>T
NM_172249.4:c.646+3861C>T
NP_001155001.1:p.Thr230Met
NP_001155002.1:p.Thr230Met
NP_001155003.1:p.Thr230Met
NP_001155004.1:p.Thr97Met
NP_001366082.1:p.Thr230Met
NP_001366083.1:p.Thr230Met
NP_001366084.1:p.Thr230Met
NP_001366085.1:p.Thr230Met
NP_001366087.1:p.Thr230Met
NP_001366088.1:p.Thr230Met
NP_001366089.1:p.Thr230Met
NP_001366090.1:p.Thr230Met
NP_001366091.1:p.Thr230Met
NP_001366092.1:p.Thr230Met
NP_001366093.1:p.Thr230Met
NP_001366094.1:p.Thr230Met
NP_001366095.1:p.Arg224Ter
NP_001366096.1:p.Thr230Met
NP_001366097.1:p.Thr230Met
NP_001366098.1:p.Thr230Met
NP_006131.2:p.Thr230Met
NP_758448.1:p.Thr230Met
NP_758449.1:p.Thr230Met
NP_758450.1:p.Thr230Met
LRG_186:g.30571C>T
NC_000023.10:g.1413263C>T
NC_000024.9:g.1363263C>T
NR_027760.3:n.869C>T

Protein change:

R224*

Links:

dbSNP: rs371464087

NCBI 1000 Genomes Browser:

rs371464087

Molecular consequence:

NM_172249.4:c.646+3861C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001161529.2:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001161530.2:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001161531.2:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001161532.2:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379153.1:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379154.1:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379155.1:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379156.1:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379158.1:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379159.1:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379160.1:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379161.1:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379162.1:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379163.1:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379164.1:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379165.1:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379167.1:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379168.1:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379169.1:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_006140.6:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_172245.4:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_172246.4:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_172247.3:c.689C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_027760.3:n.869C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001379166.1:c.670C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Surfactant metabolism dysfunction, pulmonary, 4 (SMDP4)
Synonyms:: CSF2RA DEFICIENCY; PAP DUE TO CSF2RA DEFICIENCY; PULMONARY ALVEOLAR PROTEINOSIS, CONGENITAL, 4
Identifiers:: MONDO: MONDO:0010424; MedGen: C2677877; Orphanet: 264675; OMIM: 300770

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003783805	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 1, 2022)	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

SCV003783805

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 1, 2022)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV003783805.2

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

Description

This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 230 of the CSF2RA protein (p.Thr230Met). This variant is present in population databases (no rsID available, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with CSF2RA-related conditions. ClinVar contains an entry for this variant (Variation ID: 1012852). 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: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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.

#	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 20, 2024

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