SFT2D3

SFT2 domain containing 3

Basic information

Region (hg38): 2:127701497-127705242

Links

ENSG00000173349 ∙ NCBI:84826 ∙ ∙ HGNC:28767 ∙ Uniprot:Q587I9 ∙ 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 SFT2D3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFT2D3 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in SFT2D3

This is a list of pathogenic ClinVar variants found in the SFT2D3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-127701533-C-T		not specified	Uncertain significance (Dec 28, 2022)
2-127701554-A-T		not specified	Uncertain significance (Dec 16, 2021)
2-127701586-C-T		not specified	Uncertain significance (Jun 10, 2022)
2-127701590-C-A		not specified	Uncertain significance (Jun 04, 2024)
2-127701595-G-A		not specified	Uncertain significance (Aug 01, 2022)
2-127701646-G-C		not specified	Uncertain significance (May 26, 2024)
2-127701785-T-A		not specified	Uncertain significance (Apr 15, 2024)
2-127701836-T-C		not specified	Uncertain significance (Apr 07, 2023)
2-127701872-G-T		not specified	Uncertain significance (Oct 26, 2021)
2-127701875-C-G		not specified	Uncertain significance (Dec 15, 2022)
2-127701907-C-G		not specified	Uncertain significance (Oct 27, 2021)
2-127701943-G-A		not specified	Uncertain significance (Aug 10, 2023)
2-127702015-C-T		not specified	Uncertain significance (Mar 29, 2022)
2-127702021-A-G		not specified	Uncertain significance (Jul 20, 2022)
2-127702034-C-G		not specified	Uncertain significance (Jul 15, 2021)
2-127702075-G-A		not specified	Uncertain significance (Apr 17, 2023)
2-127702076-C-T		not specified	Uncertain significance (Jan 31, 2022)
2-127702105-G-A		not specified	Uncertain significance (Feb 07, 2023)
2-127702150-G-A		not specified	Uncertain significance (Oct 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SFT2D3	protein_coding	protein_coding	ENST00000310981	1	2789

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.101	0.600	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.49	45	24.3	1.85	0.00000129	1214
Missense in Polyphen		10	5.2403	1.9083		184
Synonymous	-4.46	35	13.9	2.52	7.52e-7	539
Loss of Function	0.171	1	1.20	0.832	5.17e-8	41

LoF frequencies by population

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

Haploinsufficiency Scores

• pHI: 0.194
• ghis: 0.461

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.209

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sft2d3

Gene ontology

• Biological process: protein transport;vesicle-mediated transport
• Cellular component: integral component of membrane