SCFD2

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense		1 clinvar	99 clinvar	2 clinvar		102
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	1	102	3	0	106

Highest pathogenic variant AF is 0.0000360488

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152540.4	RefSeq	NP_689753.2	9	MANE Select
ENST00000401642.8	Ensembl	ENSP00000384182.3	9	MANE Select
ENST00000388940.8	Ensembl	ENSP00000373592.4	8	Standard
ENST00000388940.9	Ensembl	ENSP00000373592.4	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

vesicle docking involved in exocytosis
biological_process
protein transport

Molecular Function

molecular_function

Cellular Component

cellular_component

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000401642
Coding exons: 9
Length: 493094
Individuals with no LoFs: 125649
Homozygous LoFs: 1
Heterozygous LoFs: 98
Defined: 125748
p: 0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.216	364	376	0.969	0.0000179	4418
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.00035	0.00035	rare
Ashkenazi Jewish	0.00031	0.00030	rare
East Asian	0.00072	0.00071	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00033	0.00033	rare
South Asian	0.00052	0.00049	rare
Other	0.0013	0.0013	notable

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.794
RVIS EVS: -0.04
RVIS percentile EVS: 50.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.248

Gene Damage Prediction

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