SFT2D2

SFT2 domain containing 2

Basic information

Region (hg38): 1:168225938-168253021

Links

ENSG00000213064 ∙ NCBI:375035 ∙ ∙ HGNC:25140 ∙ Uniprot:O95562 ∙ 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 SFT2D2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFT2D2 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			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in SFT2D2

This is a list of pathogenic ClinVar variants found in the SFT2D2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-168226097-G-C		not specified	Uncertain significance (Jun 26, 2024)
1-168226114-A-C		not specified	Uncertain significance (May 09, 2023)
1-168226120-A-G		not specified	Uncertain significance (Jan 18, 2025)
1-168231554-A-T		not specified	Uncertain significance (Nov 21, 2022)
1-168231880-C-T		not specified	Uncertain significance (Oct 07, 2024)
1-168235174-A-C		not specified	Likely benign (Nov 07, 2022)
1-168236617-C-G		not specified	Uncertain significance (Mar 29, 2022)
1-168236725-G-A		not specified	Uncertain significance (Jan 19, 2024)
1-168236731-C-T		not specified	Uncertain significance (Jan 17, 2024)
1-168239133-A-G		not specified	Uncertain significance (Dec 03, 2024)
1-168239144-T-A		not specified	Uncertain significance (Aug 10, 2021)
1-168239144-T-G		not specified	Uncertain significance (Jan 27, 2022)
1-168239147-A-G		not specified	Uncertain significance (Feb 27, 2023)
1-168242529-T-G		not specified	Uncertain significance (Dec 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SFT2D2	protein_coding	protein_coding	ENST00000271375	8	27088

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0111	0.952	125700	0	48	125748	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.163	88	83.8	1.05	0.00000431	1025
Missense in Polyphen		18	18.468	0.97465		210
Synonymous	-0.0269	32	31.8	1.01	0.00000171	308
Loss of Function	1.81	5	11.7	0.428	5.81e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.00	0.00
East Asian	0.000761	0.000761
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000167	0.000167
Middle Eastern	0.000761	0.000761
South Asian	0.000261	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in fusion of retrograde transport vesicles derived from an endocytic compartment with the Golgi complex. {ECO:0000250|UniProtKB:P38166}.
• Pathway: TYROBP Causal Network (Consensus)

Intolerance Scores

• loftool: 0.809
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.216
• ghis: 0.596

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sft2d2

Gene ontology

• Biological process: biological_process;protein transport;vesicle-mediated transport
• Cellular component: integral component of membrane;extracellular exosome
• Molecular function: molecular_function