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GeneBe

SFTPA2

surfactant protein A2, the group of Collectins|C-type lectin domain containing

Basic information

Region (hg38): 10:79555851-79560407

Links

ENSG00000185303NCBI:729238OMIM:178642HGNC:10799Uniprot:Q8IWL1AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • idiopathic pulmonary fibrosis (Moderate), mode of inheritance: AD
  • interstitial lung disease 2 (Strong), mode of inheritance: AD
  • idiopathic pulmonary fibrosis (Limited), mode of inheritance: Unknown
  • interstitial lung disease 2 (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Interstitial lung disease 2ADOncologicSurveillance for and early diagnosis of neoplasms could allow potentially beneficial treatmentOncologic; Pulmonary19100526

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SFTPA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFTPA2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
13
clinvar
4
clinvar
17
missense
1
clinvar
18
clinvar
6
clinvar
7
clinvar
32
nonsense
0
start loss
0
frameshift
0
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
splice region
1
1
2
non coding
1
clinvar
1
clinvar
13
clinvar
15
Total 0 1 20 20 24

Variants in SFTPA2

This is a list of pathogenic ClinVar variants found in the SFTPA2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
10-79557057-G-A Benign (Nov 12, 2018)1258839
10-79557223-T-C Inborn genetic diseases Uncertain significance (Nov 09, 2022)2324613
10-79557234-GAGT-G Uncertain significance (Feb 01, 2024)3027274
10-79557259-A-T Interstitial lung disease 2 Pathogenic (Nov 19, 2021)1325405
10-79557264-C-A Interstitial lung disease 2 • Pulmonary fibrosis Pathogenic/Likely risk allele (Jun 09, 2022)13199
10-79557276-A-C Uncertain significance (Apr 06, 2020)1691338
10-79557280-C-T Interstitial lung disease 2 Uncertain significance (Aug 10, 2022)1704398
10-79557289-G-T not specified • Interstitial lung disease 2 Benign (Jul 15, 2021)227071
10-79557299-C-T SFTPA2-related disorder Benign (Nov 23, 2020)3047064
10-79557300-C-A Interstitial lung disease 2 Uncertain significance (Feb 01, 2022)1705915
10-79557301-G-A SFTPA2-related disorder Likely benign (Jul 06, 2021)3033731
10-79557306-G-A Inborn genetic diseases Uncertain significance (Nov 13, 2023)3160957
10-79557308-A-G not specified Benign (Dec 10, 2015)227070
10-79557350-A-G Likely benign (Jan 01, 2023)2640641
10-79557361-G-A Inborn genetic diseases Uncertain significance (Jun 03, 2022)3160956
10-79557363-A-G Interstitial lung disease 2 Pathogenic (Jan 01, 2009)13200
10-79557399-T-C Interstitial lung disease 2 Likely pathogenic (Feb 01, 2022)1705914
10-79557424-C-T Inborn genetic diseases • Interstitial lung disease 2 Conflicting classifications of pathogenicity (Feb 01, 2022)985062
10-79557425-G-A SFTPA2-related disorder Likely benign (May 03, 2021)3051988
10-79557426-A-T Interstitial lung disease 2 Uncertain significance (Feb 01, 2022)1705913
10-79557440-C-G Inborn genetic diseases Uncertain significance (Sep 25, 2023)3160955
10-79557444-T-A Interstitial lung disease 2 Pathogenic (Nov 18, 2021)1322020
10-79557468-G-A Inborn genetic diseases Uncertain significance (Feb 22, 2023)2486879
10-79557496-C-G Interstitial lung disease 2 Conflicting classifications of pathogenicity (Jan 01, 2024)1705909
10-79557536-G-A not specified • Interstitial lung disease 2 Benign/Likely benign (Jul 15, 2021)227069

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SFTPA2protein_codingprotein_codingENST00000372325 44546
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.009250.82412563301141257470.000453
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.161761381.280.000007651578
Missense in Polyphen5950.6131.1657590
Synonymous-2.417754.41.420.00000334519
Loss of Function1.1047.180.5573.09e-794

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00009040.0000904
Ashkenazi Jewish0.000.00
East Asian0.0005440.000544
Finnish0.003190.00319
European (Non-Finnish)0.0001500.000149
Middle Eastern0.0005440.000544
South Asian0.0003920.000392
Other0.0006520.000652

dbNSFP

Source: dbNSFP

Function
FUNCTION: In presence of calcium ions, it binds to surfactant phospholipids and contributes to lower the surface tension at the air-liquid interface in the alveoli of the mammalian lung and is essential for normal respiration.;
Disease
DISEASE: Pulmonary fibrosis, idiopathic (IPF) [MIM:178500]: A lung disease characterized by shortness of breath, radiographically evident diffuse pulmonary infiltrates, and varying degrees of inflammation and fibrosis on biopsy. In some cases, the disorder can be rapidly progressive and characterized by sequential acute lung injury with subsequent scarring and end-stage lung disease. {ECO:0000269|PubMed:19100526}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Pertussis - Homo sapiens (human);Phagosome - Homo sapiens (human);Regulation of toll-like receptor signaling pathway;Human Complement System;Surfactant metabolism;Lung fibrosis;Surfactant metabolism;Metabolism of proteins;FOXA1 transcription factor network (Consensus)

Recessive Scores

pRec
0.137

Intolerance Scores

loftool
0.523
rvis_EVS
0.62
rvis_percentile_EVS
83.25

Haploinsufficiency Scores

pHI
0.0823
hipred
N
hipred_score
0.139
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.127

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sftpa1
Phenotype
homeostasis/metabolism phenotype; hematopoietic system phenotype; immune system phenotype; respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Gene ontology

Biological process
toll-like receptor signaling pathway;respiratory gaseous exchange;developmental process;surfactant homeostasis;cellular protein metabolic process;positive regulation of phagocytosis
Cellular component
extracellular region;collagen trimer;extracellular space;multivesicular body;endoplasmic reticulum membrane;rough endoplasmic reticulum;lamellar body;clathrin-coated endocytic vesicle
Molecular function
lipopolysaccharide binding;monosaccharide binding