SCFD2

sec1 family domain containing 2

Basic information

Region (hg38): 4:52872982-53366066

Links

ENSG00000184178 ∙ NCBI:152579 ∙ ∙ HGNC:30676 ∙ Uniprot:Q8WU76 ∙ 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 SCFD2 gene.

• not_specified (87 variants)
• Autism,_susceptiblity_to (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCFD2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152540.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense		1	84	2		87
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	84	3	0

Highest pathogenic variant AF is 0.0000360488

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCFD2	protein_coding	protein_coding	ENST00000401642	9	493094

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.02e-13	0.113	125649	1	98	125748	0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.216	364	376	0.969	0.0000179	4418
Missense in Polyphen		129	129.24	0.99815		1636
Synonymous	-0.159	157	154	1.02	0.00000759	1441
Loss of Function	0.697	21	24.7	0.849	0.00000105	314

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000966	0.000963
Ashkenazi Jewish	0.000312	0.000298
East Asian	0.000716	0.000707
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000327	0.000325
Middle Eastern	0.000716	0.000707
South Asian	0.000523	0.000490
Other	0.00134	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in protein transport.

Intolerance Scores

• loftool: 0.794
• rvis_EVS: -0.04
• rvis_percentile_EVS: 50.51

Haploinsufficiency Scores

• pHI: 0.0691
• hipred: N
• hipred_score: 0.229
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.248

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scfd2

Gene ontology

• Biological process: vesicle docking involved in exocytosis;biological_process;protein transport
• Cellular component: cellular_component
• Molecular function: molecular_function