SFTA2

surfactant associated 2

Basic information

Region (hg38): 6:30931353-30955636

Previous symbols: [ "SFTPG" ]

Links

ENSG00000196260 ∙ NCBI:389376 ∙ ∙ HGNC:18386 ∙ Uniprot:Q6UW10 ∙ 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 SFTA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFTA2 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						0
missense			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in SFTA2

This is a list of pathogenic ClinVar variants found in the SFTA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-30931538-C-T		not specified	Uncertain significance (Jan 03, 2022)
6-30941070-C-G		not specified	Uncertain significance (Mar 23, 2022)
6-30941073-G-C		not specified	Uncertain significance (Sep 16, 2021)
6-30948556-C-T		not specified	Uncertain significance (Apr 27, 2022)
6-30948717-C-T		not specified	Uncertain significance (Jul 06, 2021)
6-30948735-C-T		not specified	Uncertain significance (Oct 12, 2021)
6-30948801-G-A		not specified	Uncertain significance (Dec 22, 2023)
6-30948844-A-G		not specified	Uncertain significance (Nov 08, 2022)
6-30948850-G-T		not specified	Uncertain significance (Aug 02, 2021)
6-30948867-C-T		not specified	Uncertain significance (Nov 03, 2023)
6-30948868-G-A			Benign (May 10, 2018)
6-30948895-A-C		not specified	Uncertain significance (Feb 22, 2023)
6-30948921-G-A		not specified	Uncertain significance (Dec 07, 2021)
6-30948933-C-A		not specified	Uncertain significance (Jun 07, 2023)
6-30948940-C-T		not specified	Uncertain significance (Sep 22, 2022)
6-30948970-G-A		not specified	Likely benign (Dec 08, 2023)
6-30949045-G-A		not specified	Uncertain significance (Mar 15, 2024)
6-30949069-G-A		not specified	Uncertain significance (Mar 07, 2024)
6-30949102-C-T		not specified	Uncertain significance (Nov 03, 2022)
6-30949185-G-A		not specified	Uncertain significance (Dec 09, 2023)
6-30949214-A-C		not specified	Uncertain significance (Apr 28, 2022)
6-30949224-A-G		not specified	Uncertain significance (Mar 02, 2023)
6-30949276-A-G		not specified	Uncertain significance (Jul 19, 2022)
6-30949317-C-G		not specified	Uncertain significance (Mar 19, 2024)
6-30949352-C-A		not specified	Uncertain significance (Nov 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SFTA2	protein_coding	protein_coding	ENST00000359086	3	823

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0364	0.648	121768	0	8	121776	0.0000328

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.308	33	38.4	0.860	0.00000182	483
Missense in Polyphen		1	0.89137	1.1219		15
Synonymous	0.220	16	17.2	0.932	8.31e-7	165
Loss of Function	0.382	2	2.67	0.748	1.13e-7	33

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000438	0.000438
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000438	0.000438
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative surfactant protein. {ECO:0000305}.

Intolerance Scores

• loftool: 0.436
• rvis_EVS: 0.21
• rvis_percentile_EVS: 67.72

Haploinsufficiency Scores

• pHI: 0.190
• hipred: N
• hipred_score: 0.184
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.105

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sfta2

Gene ontology

• Cellular component: extracellular region;Golgi apparatus;transport vesicle