SFTPA2

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

Basic information

Region (hg38): 10:79555851-79560407

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
• 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

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.

• not provided (27 variants)
• not specified (11 variants)
• Interstitial lung disease 2 (11 variants)
• Inborn genetic diseases (10 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.

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				2	5	7
missense		2	12		6	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1		13	14
Total	0	2	13	2	24

Highest pathogenic variant AF is 0.000132

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)
10-79557223-T-C		Inborn genetic diseases	Uncertain significance (Nov 09, 2022)
10-79557234-GAGT-G			Uncertain significance (Feb 01, 2024)
10-79557259-A-T		Interstitial lung disease 2	Pathogenic (Nov 19, 2021)
10-79557264-C-A		Interstitial lung disease 2 • Pulmonary fibrosis	Pathogenic/Likely risk allele (Jun 09, 2022)
10-79557276-A-C			Uncertain significance (Apr 06, 2020)
10-79557280-C-T		Interstitial lung disease 2	Uncertain significance (Aug 10, 2022)
10-79557289-G-T		not specified • Interstitial lung disease 2	Benign (Jul 15, 2021)
10-79557299-C-T		SFTPA2-related disorder	Benign (Nov 23, 2020)
10-79557300-C-A		Interstitial lung disease 2	Uncertain significance (Feb 01, 2022)
10-79557301-G-A		SFTPA2-related disorder	Likely benign (Jul 06, 2021)
10-79557306-G-A		Inborn genetic diseases	Uncertain significance (Nov 13, 2023)
10-79557308-A-G		not specified	Benign (Dec 10, 2015)
10-79557350-A-G			Likely benign (Jan 01, 2023)
10-79557361-G-A		Inborn genetic diseases	Uncertain significance (Jun 03, 2022)
10-79557363-A-G		Interstitial lung disease 2	Pathogenic (Jan 01, 2009)
10-79557399-T-C		Interstitial lung disease 2	Likely pathogenic (Feb 01, 2022)
10-79557424-C-T		Inborn genetic diseases • Interstitial lung disease 2	Conflicting classifications of pathogenicity (Feb 01, 2022)
10-79557425-G-A		SFTPA2-related disorder	Likely benign (May 03, 2021)
10-79557426-A-T		Interstitial lung disease 2	Uncertain significance (Feb 01, 2022)
10-79557440-C-G		Inborn genetic diseases	Uncertain significance (Sep 25, 2023)
10-79557444-T-A		Interstitial lung disease 2	Pathogenic (Nov 18, 2021)
10-79557468-G-A		Inborn genetic diseases	Uncertain significance (Feb 22, 2023)
10-79557496-C-G		Interstitial lung disease 2	Conflicting classifications of pathogenicity (Jan 01, 2024)
10-79557536-G-A		not specified • Interstitial lung disease 2	Benign/Likely benign (Jul 15, 2021)

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

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