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GeneBe

SFTPA1

surfactant protein A1, the group of C-type lectin domain containing|Collectins

Basic information

Region (hg38): 10:79610938-79615455

Previous symbols: [ "SFTP1" ]

Links

ENSG00000122852NCBI:653509OMIM:178630HGNC:10798Uniprot:Q8IWL2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Interstitial lung disease 1AD/AROncologicSurveillance for and early diagnosis of lung cancer could allow potentially beneficial treatmentOncologic; Pulmonary26792177; 30854216; 31601679; 32855221

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SFTPA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFTPA1 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
14
clinvar
5
clinvar
19
missense
23
clinvar
5
clinvar
2
clinvar
30
nonsense
2
clinvar
2
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
3
clinvar
12
clinvar
15
Total 0 0 25 22 19

Variants in SFTPA1

This is a list of pathogenic ClinVar variants found in the SFTPA1 region.

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

Position Type Phenotype Significance ClinVar
10-79611646-T-A SFTPA1-related disorder Likely benign (Aug 22, 2019)3053251
10-79611647-G-A SFTPA1-related disorder Likely benign (Aug 22, 2019)3053677
10-79611650-G-A SFTPA1-related disorder Likely benign (Nov 22, 2019)3048596
10-79611665-A-T Benign (Nov 12, 2018)1260769
10-79611843-G-T SFTPA1-related disorder Likely benign (May 20, 2020)3054609
10-79611851-A-C not specified Likely benign (Dec 16, 2015)227944
10-79611881-T-C not specified • See cases • SFTPA1-related disorder Benign/Likely benign (Jun 09, 2021)227942
10-79611897-C-T SFTPA1-related disorder Likely benign (Mar 16, 2021)3030634
10-79611899-T-A not specified Uncertain significance (Jun 22, 2023)2605818
10-79611916-G-C not specified Uncertain significance (Dec 14, 2016)373663
10-79611924-C-T SFTPA1-related disorder Likely benign (Oct 18, 2019)744040
10-79611942-C-T not specified • SFTPA1-related disorder Benign (Nov 04, 2019)227061
10-79611945-C-A SFTPA1-related disorder Likely benign (Nov 13, 2020)3030714
10-79611948-G-A SFTPA1-related disorder Likely benign (Sep 30, 2022)3043686
10-79611960-C-G not specified Uncertain significance (Jan 29, 2016)229244
10-79611960-C-T SFTPA1-related disorder Likely benign (Feb 08, 2021)3055008
10-79611973-C-G not specified Benign/Likely benign (Jun 09, 2021)227062
10-79612324-C-T Likely benign (Dec 31, 2019)786416
10-79612325-A-G not specified • SFTPA1-related disorder Benign (Oct 21, 2019)165197
10-79612365-C-T not specified Uncertain significance (Dec 19, 2022)2337220
10-79612410-C-G not specified Benign (May 01, 2024)165198
10-79612416-G-A not specified Uncertain significance (Feb 23, 2023)2460460
10-79612431-G-A Proximal 16p11.2 microdeletion syndrome Uncertain significance (Jan 08, 2020)1691337
10-79612475-CG-C Benign (Nov 12, 2018)1270909
10-79612689-T-C Benign (Nov 12, 2018)1235406

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SFTPA1protein_codingprotein_codingENST00000419470 54502
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0003680.6331257050391257440.000155
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.7141731491.160.000008061675
Missense in Polyphen6255.8881.1094645
Synonymous-0.008325655.91.000.00000333536
Loss of Function0.68068.090.7423.47e-7106

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001250.00125
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00002640.0000264
Middle Eastern0.000.00
South Asian0.000.00
Other0.0004890.000489

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. Enhances the expression of MYO18A/SP-R210 on alveolar macrophages (By similarity). {ECO:0000250|UniProtKB:P35242}.;
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. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Respiratory distress syndrome in premature infants (RDS) [MIM:267450]: A lung disease affecting usually premature newborn infants. It is characterized by deficient gas exchange, diffuse atelectasis, high-permeability lung edema and fibrin-rich alveolar deposits called 'hyaline membranes'. {ECO:0000269|PubMed:10762543}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry. The association between SFTPA1 alleles and respiratory distress syndrome in premature infants is dependent on a variation Ile to Thr at position 131 in SFTPB.;
Pathway
Pertussis - Homo sapiens (human);Phagosome - Homo sapiens (human);Human Complement System;Surfactant metabolism;Lung fibrosis;Surfactant metabolism;Metabolism of proteins;FOXA1 transcription factor network;Endogenous TLR signaling (Consensus)

Recessive Scores

pRec
0.405

Intolerance Scores

loftool
0.205
rvis_EVS
0.46
rvis_percentile_EVS
78.46

Haploinsufficiency Scores

pHI
0.0708
hipred
N
hipred_score
0.112
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.674

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;lipid transport;respiratory gaseous exchange;opsonization;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;lipid transporter activity;protein binding;monosaccharide binding