SFTPA1

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

Basic information

Region (hg38): 10:79610938-79615455

Previous symbols: [ "SFTP1" ]

Links

ENSG00000122852 ∙ NCBI:653509 ∙ OMIM:178630 ∙ HGNC:10798 ∙ Uniprot:Q8IWL2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Interstitial lung disease 1	AD/AR	Oncologic	Surveillance for and early diagnosis of lung cancer could allow potentially beneficial treatment	Oncologic; Pulmonary	26792177; 30854216; 31601679; 32855221

ClinVar

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

• not provided (26 variants)
• not specified (21 variants)
• Inborn genetic diseases (10 variants)
• Interstitial lung disease 1 (3 variants)
• Proximal 16p11.2 microdeletion syndrome (1 variants)
• Pulmonary fibrosis, idiopathic, susceptibility to (1 variants)
• Respiratory distress associated with prematurity (1 variants)
• Interstitial lung disease 2 (1 variants)
• See cases (1 variants)

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				5	5	10
missense			20	5	2	27
nonsense			2			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					12	12
Total	0	0	22	10	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)
10-79611647-G-A		SFTPA1-related disorder	Likely benign (Aug 22, 2019)
10-79611650-G-A		SFTPA1-related disorder	Likely benign (Nov 22, 2019)
10-79611665-A-T			Benign (Nov 12, 2018)
10-79611843-G-T		SFTPA1-related disorder	Likely benign (May 20, 2020)
10-79611851-A-C		not specified	Likely benign (Dec 16, 2015)
10-79611881-T-C		not specified • See cases • SFTPA1-related disorder	Benign/Likely benign (Jun 09, 2021)
10-79611897-C-T		SFTPA1-related disorder	Likely benign (Mar 16, 2021)
10-79611899-T-A		not specified	Uncertain significance (Jun 22, 2023)
10-79611916-G-C		not specified	Uncertain significance (Dec 14, 2016)
10-79611924-C-T		SFTPA1-related disorder	Likely benign (Oct 18, 2019)
10-79611942-C-T		not specified • SFTPA1-related disorder	Benign (Nov 04, 2019)
10-79611945-C-A		SFTPA1-related disorder	Likely benign (Nov 13, 2020)
10-79611948-G-A		SFTPA1-related disorder	Likely benign (Sep 30, 2022)
10-79611960-C-G		not specified	Uncertain significance (Jan 29, 2016)
10-79611960-C-T		SFTPA1-related disorder	Likely benign (Feb 08, 2021)
10-79611973-C-G		not specified	Benign/Likely benign (Jun 09, 2021)
10-79612324-C-T			Likely benign (Dec 31, 2019)
10-79612325-A-G		not specified • SFTPA1-related disorder	Benign (Oct 21, 2019)
10-79612365-C-T		not specified	Uncertain significance (Dec 19, 2022)
10-79612410-C-G		not specified	Benign (Dec 31, 2019)
10-79612416-G-A		not specified	Uncertain significance (Feb 23, 2023)
10-79612431-G-A		Proximal 16p11.2 microdeletion syndrome	Uncertain significance (Jan 08, 2020)
10-79612475-CG-C			Benign (Nov 12, 2018)
10-79612689-T-C			Benign (Nov 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SFTPA1	protein_coding	protein_coding	ENST00000419470	5	4502

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000368	0.633	125705	0	39	125744	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.714	173	149	1.16	0.00000806	1675
Missense in Polyphen		62	55.888	1.1094		645
Synonymous	-0.00832	56	55.9	1.00	0.00000333	536
Loss of Function	0.680	6	8.09	0.742	3.47e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00125	0.00125
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000489	0.000489

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

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.674

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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