SFTPA2

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

Basic information

Region (hg38): 10:79555852-79560407

Links

ENSG00000185303

∙ NCBI:729238 ∙ OMIM:178642 ∙ HGNC:10799 ∙ Uniprot:Q8IWL1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Interstitial lung disease 2	AD	Oncologic	Surveillance for and early diagnosis of neoplasms could allow potentially beneficial treatment	Oncologic; Pulmonary	19100526

ClinVar

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

Inborn_genetic_diseases (34 variants)
SFTPA2-related_disorder (23 variants)
not_provided (19 variants)
Interstitial_lung_disease_2 (14 variants)
not_specified (6 variants)
Mullegama-Klein-Martinez_syndrome (2 variants)
Pulmonary_fibrosis (1 variants)

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. These statistics are base on transcript: NM_001098668.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	10 clinvar	6 clinvar	18
missense	4 clinvar	3 clinvar	40 clinvar	8 clinvar	3 clinvar	58
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	4	3	43	18	9

Highest pathogenic variant AF is 0.000185932

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SFTPA2	protein_coding	protein_coding	ENST00000372325	4	4546

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00925	0.824	125633	0	114	125747	0.000453

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.16	176	138	1.28	0.00000765	1578
Missense in Polyphen		59	50.613	1.1657		590
Synonymous	-2.41	77	54.4	1.42	0.00000334	519
Loss of Function	1.10	4	7.18	0.557	3.09e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000544	0.000544
Finnish	0.00319	0.00319
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000544	0.000544
South Asian	0.000392	0.000392
Other	0.000652	0.000652

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

	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;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