SFTPD

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

Basic information

Region (hg38): 10:79937467-79982614

Previous symbols: [ "SFTP4" ]

Links

ENSG00000133661 ∙ NCBI:6441 ∙ OMIM:178635 ∙ HGNC:10803 ∙ Uniprot:P35247 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFTPD 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					3	3
missense			17	1	5	23
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					4	4
Total	0	0	18	1	12

Variants in SFTPD

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

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

Position	Type	Phenotype	Significance	ClinVar
10-79937897-A-AT		SFTPD-related disorder	Uncertain significance (Dec 19, 2022)
10-79938055-C-T		not specified	Benign (Feb 21, 2013)
10-79938062-A-G		not specified	Benign (Feb 21, 2013)
10-79938085-C-A		not specified	Uncertain significance (Jan 31, 2023)
10-79938097-C-T		not specified	Uncertain significance (Oct 11, 2017)
10-79938112-A-T		not specified	Benign (Feb 21, 2013)
10-79938155-C-T		SFTPD-related disorder	Benign (Dec 19, 2019)
10-79938243-AAGTC-A		not specified	Benign (Mar 28, 2016)
10-79938341-G-A			Benign (Nov 12, 2018)
10-79940713-T-C		not specified	Uncertain significance (Aug 28, 2023)
10-79940788-T-C		not specified	Uncertain significance (May 31, 2022)
10-79941509-C-A		not specified	Uncertain significance (Jan 07, 2022)
10-79941767-T-C			Benign (Nov 12, 2018)
10-79941966-T-C		not specified	Benign (Nov 12, 2018)
10-79941974-G-C		not specified	Uncertain significance (Feb 06, 2023)
10-79942019-G-A		not specified	Uncertain significance (Sep 30, 2021)
10-79942020-C-T		SFTPD-related disorder	Uncertain significance (Dec 24, 2023)
10-79942421-T-C		not specified	Uncertain significance (Feb 16, 2023)
10-79942454-G-C		not specified	Benign (Feb 21, 2013)
10-79942487-C-T		not specified	Uncertain significance (May 01, 2024)
10-79942782-C-T		not specified	Benign (Feb 21, 2013)
10-79942875-C-A		not specified	Uncertain significance (Nov 10, 2022)
10-79946452-C-T		not specified • SFTPD-related disorder	Benign (Oct 05, 2017)
10-79946481-C-T		not specified	Uncertain significance (May 09, 2023)
10-79946487-C-T		not specified	Uncertain significance (Sep 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SFTPD	protein_coding	protein_coding	ENST00000372292	7	44875

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000749	0.925	125661	1	86	125748	0.000346

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.578	190	214	0.889	0.0000111	2369
Missense in Polyphen		60	78.387	0.76543		854
Synonymous	1.06	73	85.5	0.854	0.00000484	814
Loss of Function	1.63	9	16.0	0.561	7.62e-7	190

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00260	0.00254
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000326	0.000326
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000326	0.000326
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Contributes to the lung's defense against inhaled microorganisms, organic antigens and toxins. Interacts with compounds such as bacterial lipopolysaccharides, oligosaccharides and fatty acids and modulates leukocyte action in immune response. May participate in the extracellular reorganization or turnover of pulmonary surfactant. Binds strongly maltose residues and to a lesser extent other alpha-glucosyl moieties. {ECO:0000269|PubMed:23478426}.
• Pathway: Phagosome - Homo sapiens (human);Regulation of toll-like receptor signaling pathway;Surfactant metabolism;Surfactant metabolism;Metabolism of proteins;FOXA1 transcription factor network;Regulation of retinoblastoma protein (Consensus)

Recessive Scores

• pRec: 0.255

Intolerance Scores

• loftool: 0.367
• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.65

Haploinsufficiency Scores

• pHI: 0.0499
• hipred: N
• hipred_score: 0.334

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.656

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sftpd
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; respiratory system phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: regulation of cytokine production;toll-like receptor signaling pathway;receptor-mediated endocytosis;respiratory gaseous exchange;developmental process;negative regulation of T cell proliferation;defense response to bacterium;surfactant homeostasis;induction of bacterial agglutination;cellular protein metabolic process;negative regulation of interleukin-2 biosynthetic process;innate immune response;macrophage chemotaxis;lung alveolus development;positive regulation of phagocytosis;regulation of immune response;negative regulation by host of symbiont molecular function;reactive oxygen species metabolic process;regulation of adhesion of symbiont to host epithelial cell
• Cellular component: extracellular region;collagen trimer;extracellular space;lysosome;multivesicular body;endoplasmic reticulum membrane;rough endoplasmic reticulum;endocytic vesicle;clathrin-coated endocytic vesicle
• Molecular function: lipopolysaccharide binding;protein binding;carbohydrate binding;identical protein binding;monosaccharide binding