SFT2D1

SFT2 domain containing 1

Basic information

Region (hg38): 6:166319727-166342576

Previous symbols: [ "C6orf83" ]

Links

ENSG00000198818 ∙ NCBI:113402 ∙ ∙ HGNC:21102 ∙ Uniprot:Q8WV19 ∙ 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 SFT2D1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFT2D1 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			7	2		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	2	0

Variants in SFT2D1

This is a list of pathogenic ClinVar variants found in the SFT2D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-166320236-C-T		not specified	Uncertain significance (Dec 05, 2022)
6-166324540-G-C		not specified	Uncertain significance (Jun 10, 2022)
6-166324574-C-G		not specified	Likely benign (Oct 12, 2021)
6-166329522-A-G		not specified	Uncertain significance (Jun 18, 2021)
6-166329528-C-T		not specified	Uncertain significance (Nov 30, 2021)
6-166329529-C-T		not specified	Uncertain significance (Nov 07, 2022)
6-166329561-C-A		not specified	Uncertain significance (Aug 13, 2021)
6-166330178-C-T		not specified	Likely benign (Oct 26, 2022)
6-166342468-C-T		not specified	Uncertain significance (Mar 30, 2024)
6-166342472-G-T		not specified	Uncertain significance (Oct 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SFT2D1	protein_coding	protein_coding	ENST00000361731	8	22864

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00162	0.896	125716	0	30	125746	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.313	72	79.9	0.902	0.00000388	1012
Missense in Polyphen		8	14.429	0.55446		196
Synonymous	-0.598	37	32.7	1.13	0.00000187	296
Loss of Function	1.42	6	11.1	0.540	4.71e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000187	0.000182
Ashkenazi Jewish	0.00	0.00
East Asian	0.000825	0.000816
Finnish	0.0000930	0.0000924
European (Non-Finnish)	0.0000374	0.0000352
Middle Eastern	0.000825	0.000816
South Asian	0.000135	0.000131
Other	0.000171	0.000163

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}.

Recessive Scores

• pRec: 0.0651

Intolerance Scores

• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.282
• ghis: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.519

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sft2d1

Gene ontology

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