NM_001098668.4(SFTPA2):c.680T>G (p.Met227Arg) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 6, 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:: RCV002254436.2

Allele description [Variation Report for NM_001098668.4(SFTPA2):c.680T>G (p.Met227Arg)]

NM_001098668.4(SFTPA2):c.680T>G (p.Met227Arg)

Gene:

SFTPA2:surfactant protein A2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q22.3

Genomic location:

Preferred name:

NM_001098668.4(SFTPA2):c.680T>G (p.Met227Arg)

HGVS:

NC_000010.11:g.79557276A>C
NG_013046.1:g.8132T>G
NM_001098668.4:c.680T>GMANE SELECT
NM_001320813.2:c.680T>G
NM_001320814.1:c.710T>G
NP_001092138.1:p.Met227Arg
NP_001307742.1:p.Met227Arg
NP_001307743.1:p.Met237Arg
NC_000010.10:g.81317032A>C
NM_001098668.2:c.680T>G

Protein change:

M227R

Links:

dbSNP: rs2132045334

NCBI 1000 Genomes Browser:

rs2132045334

Molecular consequence:

NM_001098668.4:c.680T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001320813.2:c.680T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001320814.1:c.710T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002525600	Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Apr 6, 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

SCV002525600

Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Apr 6, 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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital, SCV002525600.1

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

Description

The p.Met227Arg variant substitutes the methionine for arginine at position 227 within the last exon of SFTPA2. This variant has not been observed in large population cohorts (0 of 251,474 alleles; Genome Aggregation Database v2.1). This variant is absent from the medical literature and the patient database ClinVar. This is a moderately conserved amino acid. Some in silico tools predict this change is damaging (EIGEN, FATHMM-MKL, MutationTaster and SIFT), while others predict this change is tolerated (DANN, M-CAP, MVP, PrimateAI and REVEL). SFTPA2 encodes the pulmonary-associated surfactant protein A2. The 248-amino acid (aa) SFTPA2 protein contains a collagen-like region (aa 28-99), a neck domain (aa 100-133), and a C-terminal carbohydrate-recognition domain (aa 134-248) (PMID: 23056344 and UniProtKB - Q8IWL1). Pathogenic variants (p.Gly231Val; p.Gly231Arg) and benign variants (p.Gln 223Lys) have been reported in this region of the carbohydrate-recognition domain (PMID: 26568241).

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

Last Updated: Dec 24, 2023

ClinVar

Relating variation to medicine