NM_001317778.2(SFTPC):c.553G>A (p.Glu185Lys) AND not provided

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 31, 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:: RCV001898005.2

Allele description

NM_001317778.2(SFTPC):c.553G>A (p.Glu185Lys)

Gene:

SFTPC:surfactant protein C [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8p21.3

Genomic location:

Preferred name:

NM_001317778.2(SFTPC):c.553G>A (p.Glu185Lys)

HGVS:

NC_000008.11:g.22164018G>A
NG_016968.1:g.7348G>A
NG_029659.1:g.3879G>A
NM_001172357.2:c.553G>A
NM_001172410.2:c.571G>A
NM_001317778.2:c.553G>AMANE SELECT
NM_001317779.2:c.412G>A
NM_001317780.2:c.553G>A
NM_001385653.1:c.571G>A
NM_001385654.1:c.571G>A
NM_001385655.1:c.571G>A
NM_001385656.1:c.553G>A
NM_001385657.1:c.553G>A
NM_001385658.1:c.553G>A
NM_001385659.1:c.553G>A
NM_001385660.1:c.412G>A
NM_003018.4:c.571G>A
NP_001165828.1:p.Glu185Lys
NP_001165881.1:p.Glu191Lys
NP_001304707.1:p.Glu185Lys
NP_001304708.1:p.Glu138Lys
NP_001304709.1:p.Glu185Lys
NP_001372582.1:p.Glu191Lys
NP_001372583.1:p.Glu191Lys
NP_001372584.1:p.Glu191Lys
NP_001372585.1:p.Glu185Lys
NP_001372586.1:p.Glu185Lys
NP_001372587.1:p.Glu185Lys
NP_001372588.1:p.Glu185Lys
NP_001372589.1:p.Glu138Lys
NP_003009.2:p.Glu191Lys
NC_000008.10:g.22021531G>A

Protein change:

E138K

Links:

dbSNP: rs200839715

NCBI 1000 Genomes Browser:

rs200839715

Molecular consequence:

NM_001172357.2:c.553G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001172410.2:c.571G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001317778.2:c.553G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001317779.2:c.412G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001317780.2:c.553G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001385653.1:c.571G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001385654.1:c.571G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001385655.1:c.571G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001385656.1:c.553G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001385657.1:c.553G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001385658.1:c.553G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001385659.1:c.553G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001385660.1:c.412G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_003018.4:c.571G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002163284	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 31, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25657025, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002163284

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 31, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Genotype alone does not predict the clinical course of SFTPC deficiency in paediatric patients.

Kröner C, Reu S, Teusch V, Schams A, Grimmelt AC, Barker M, Brand J, Gappa M, Kitz R, Kramer BW, Lange L, Lau S, Pfannenstiel C, Proesmans M, Seidenberg J, Sismanlar T, Aslan AT, Werner C, Zielen S, Zarbock R, Brasch F, Lohse P, et al.

Eur Respir J. 2015 Jul;46(1):197-206. doi: 10.1183/09031936.00129414. Epub 2015 Feb 5.

PubMed [citation]

PMID:: 25657025

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, SCV002163284.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 191 of the SFTPC protein (p.Glu191Lys). This variant is present in population databases (rs200839715, gnomAD 0.02%). This missense change has been observed in individual(s) with clinical features of SFTPC deficiency (PMID: 25657025). ClinVar contains an entry for this variant (Variation ID: 1389667). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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: Dec 24, 2023

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