SFTPD

protein-coding

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

Gene summary

The protein encoded by this gene is part of the innate immune response, protecting the lungs against inhaled microorganisms and chemicals. The encoded protein may also be involved in surfactant metabolism. [provided by RefSeq, Jul 2015]

Previous symbols:

SFTP4

MANE transcript

NM_003019.5

Inheritance

—

ClinVar variants

U:34B:5

Top phenotype

SFTPD-related disorder

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr10:79,937,467-79,982,614

External References & Databases

Ensembl (ENSG00000133661)

Transcript & Mutation Effects

hg38 • Region Span ~45.1 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SFTPD variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 32

SFTPD-related disorderTotal: 5

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003019.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar		2 clinvar	4
missense			29 clinvar	2 clinvar	1 clinvar	32
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	34	2	3	39

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 67 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003019.5	RefSeq	NP_003010.4	7	MANE Select
ENST00000372292.8	Ensembl	ENSP00000361366.3	7	MANE Select
ENST00000444384.3	Ensembl	ENSP00000394325.1	6	Standard
ENST00000865181.1	Ensembl	ENSP00000535240.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Phagosome - Homo sapiens (human)
Regulation of toll-like receptor signaling pathway
Surfactant metabolism
Surfactant metabolism
Metabolism of proteins

Biological Process

regulation of cytokine production
toll-like receptor signaling pathway
receptor-mediated endocytosis
respiratory gaseous exchange
developmental process

Molecular Function

lipopolysaccharide binding
protein binding
carbohydrate binding
identical protein binding
monosaccharide binding

Cellular Component

extracellular region
collagen trimer
extracellular space
lysosome
multivesicular body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372292
Coding exons: 7
Length: 44875
Individuals with no LoFs: 125661
Homozygous LoFs: 1
Heterozygous LoFs: 86
Defined: 125748
p: 0.000346

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.578	190	214	0.889	0.0000111	2369
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0018	0.0017	notable
Latino/Admixed American	0.00081	0.00081	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00033	0.00033	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.000098	0.000098	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.255

Intolerance Scores

LoFtool: 0.367
RVIS EVS: 0.75
RVIS percentile EVS: 86.65

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.656

Gene Damage Prediction

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