SFTPB

surfactant protein B

Basic information

Region (hg38): 2:85657313-85668741

Previous symbols: [ "SFTP3" ]

Links

ENSG00000168878 ∙ NCBI:6439 ∙ OMIM:178640 ∙ HGNC:10801 ∙ Uniprot:P07988 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• surfactant metabolism dysfunction, pulmonary, 1 (Strong), mode of inheritance: AR
• surfactant metabolism dysfunction, pulmonary, 1 (Supportive), mode of inheritance: AR
• surfactant metabolism dysfunction, pulmonary, 1 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Surfactant metabolism dysfunction, pulmonary 1	AR	Pulmonary	Lung transplant has been reported as effective in individuals with surfactant B deficiency, and without transplant, the disorder is typically fatal	Pulmonary	8421459; 1341413; 8021783; 8071741; 8163685; 7491219; 7647155; 9086529; 9042125; 9506635; 10571948; 10378403; 10365365; 9927351; 11041444; 10960490; 11063734; 10712351; 10663288; 11282516; 11341756; 12784301; 17011330; 17391469; 17109726; 18558554; 19647838; 19220077; 22884059; 23625987

ClinVar

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

• not provided (5 variants)
• Hereditary pulmonary alveolar proteinosis (4 variants)
• Surfactant metabolism dysfunction, pulmonary, 1 (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFTPB 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			1	23	2	26
missense	2	2	50	8	3	65
nonsense	2					2
start loss						0
frameshift	4	2	1			7
inframe indel			1	1		2
splice donor/acceptor (+/-2bp)	1	3				4
splice region		1	4	2	1	8
non coding			15	19	27	61
Total	9	7	68	51	32

Highest pathogenic variant AF is 0.000243

Variants in SFTPB

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

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

Position	Type	Phenotype	Significance	ClinVar
2-85657336-T-G		Surfactant metabolism dysfunction, pulmonary, 1	Uncertain significance (Jan 12, 2018)
2-85657529-C-T		Surfactant metabolism dysfunction, pulmonary, 1	Uncertain significance (Jan 13, 2018)
2-85657559-G-T		Surfactant metabolism dysfunction, pulmonary, 1	Uncertain significance (Jan 12, 2018)
2-85657640-G-A		Surfactant metabolism dysfunction, pulmonary, 1	Uncertain significance (Jan 13, 2018)
2-85657790-C-T		Surfactant metabolism dysfunction, pulmonary, 1	Likely benign (Jan 13, 2018)
2-85657801-G-A		Surfactant metabolism dysfunction, pulmonary, 1	Likely benign (Jan 13, 2018)
2-85657825-G-T		Surfactant metabolism dysfunction, pulmonary, 1	Likely benign (Jan 13, 2018)
2-85657829-A-C		Surfactant metabolism dysfunction, pulmonary, 1	Uncertain significance (Jan 13, 2018)
2-85657854-C-T		Surfactant metabolism dysfunction, pulmonary, 1	Likely benign (Jan 13, 2018)
2-85657855-G-A		Surfactant metabolism dysfunction, pulmonary, 1	Benign (Jan 13, 2018)
2-85657897-C-T		Surfactant metabolism dysfunction, pulmonary, 1	Uncertain significance (Jan 13, 2018)
2-85657946-G-C		Surfactant metabolism dysfunction, pulmonary, 1	Uncertain significance (Jan 13, 2018)
2-85658062-A-T		Surfactant metabolism dysfunction, pulmonary, 1	Likely benign (Jan 12, 2018)
2-85658095-C-T		Surfactant metabolism dysfunction, pulmonary, 1	Uncertain significance (Jan 12, 2018)
2-85658111-G-T		Surfactant metabolism dysfunction, pulmonary, 1	Likely benign (Jan 12, 2018)
2-85658204-A-G		Surfactant metabolism dysfunction, pulmonary, 1	Likely benign (Jan 13, 2018)
2-85658214-T-C		Surfactant metabolism dysfunction, pulmonary, 1	Uncertain significance (Jan 12, 2018)
2-85658513-T-G		Surfactant metabolism dysfunction, pulmonary, 1	Benign (Jan 12, 2018)
2-85658780-C-T		Surfactant metabolism dysfunction, pulmonary, 1	Uncertain significance (Aug 12, 2020)
2-85658800-G-A		Surfactant metabolism dysfunction, pulmonary, 1	Uncertain significance (Jan 12, 2018)
2-85658845-G-A		Surfactant metabolism dysfunction, pulmonary, 1	Benign (Jan 12, 2018)
2-85661170-A-G			Benign (Feb 21, 2019)
2-85661480-T-A		Hereditary pulmonary alveolar proteinosis	Uncertain significance (Sep 19, 2018)
2-85661481-C-T		Surfactant metabolism dysfunction, pulmonary, 1 • Hereditary pulmonary alveolar proteinosis	Uncertain significance (Oct 29, 2021)
2-85661483-G-C		Surfactant metabolism dysfunction, pulmonary, 1	Likely benign (Jan 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SFTPB	protein_coding	protein_coding	ENST00000393822	10	11428

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000259	0.997	125664	0	84	125748	0.000334

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.597	202	227	0.889	0.0000134	2513
Missense in Polyphen		31	45.572	0.68024		578
Synonymous	0.489	94	100	0.938	0.00000659	785
Loss of Function	2.59	10	23.6	0.424	0.00000121	238

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000398	0.000388
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000561	0.000554
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Pulmonary surfactant-associated proteins promote alveolar stability by lowering the surface tension at the air- liquid interface in the peripheral air spaces. SP-B increases the collapse pressure of palmitic acid to nearly 70 millinewtons per meter.
• Disease: DISEASE: Pulmonary surfactant metabolism dysfunction 1 (SMDP1) [MIM:265120]: A rare lung disorder due to impaired surfactant homeostasis. It is characterized by alveolar filling with floccular material that stains positive using the periodic acid- Schiff method and is derived from surfactant phospholipids and protein components. Excessive lipoproteins accumulation in the alveoli results in severe respiratory distress. {ECO:0000269|PubMed:7491219}. Note=The disease is caused by mutations 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:11063734}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry. A variation Ile to Thr at position 131 influences the association between specific alleles of SFTPA1 and respiratory distress syndrome in premature infants.
• Pathway: Surfactant metabolism;Surfactant metabolism;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.235

Intolerance Scores

• loftool: 0.256
• rvis_EVS: 0.71
• rvis_percentile_EVS: 85.68

Haploinsufficiency Scores

• pHI: 0.192
• hipred: N
• hipred_score: 0.233
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0878

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sftpb
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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: sphingolipid metabolic process;respiratory gaseous exchange;animal organ morphogenesis;cellular protein metabolic process
• Cellular component: extracellular region;extracellular space;nucleoplasm;lysosome;multivesicular body;endoplasmic reticulum membrane;lamellar body;clathrin-coated endocytic vesicle;alveolar lamellar body;multivesicular body lumen