SCOC

protein-coding

short coiled-coil protein

Gene summary

This gene encodes a short coiled-coiled domain-containing protein that localizes to the Golgi apparatus. The encoded protein interacts with ADP-ribosylation factor-like proteins. Pseudogenes of this gene are found on chromosomes 1 and 14. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]

MANE transcript

NM_001153484.2

Inheritance

—

ClinVar variants

U:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chr4:140,257,286-140,385,728

External References & Databases

Ensembl (ENSG00000153130)

Transcript & Mutation Effects

hg38 • Region Span ~128.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SCOC variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 6

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001153484.2. Only rare variants are included.

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			2 clinvar			2
missense			5 clinvar			5
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	9	0	0	9

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 77 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001153484.2	RefSeq	NP_001146956.2	3	MANE Select
ENST00000608372.6	Ensembl	ENSP00000477352.2	3	MANE Select
NM_001153446.1	RefSeq	NP_001146918.1	4	Standard
NM_001153552.2	RefSeq	NP_001147024.2	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vesicle-mediated transport
Membrane Trafficking
Retrograde transport at the Trans-Golgi-Network
Intra-Golgi and retrograde Golgi-to-ER traffic

Biological Process

positive regulation of macroautophagy
regulation of protein complex stability

Molecular Function

protein binding

Cellular Component

Golgi membrane
nucleoplasm
endosome
Golgi apparatus
trans-Golgi network

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000608372
Coding exons: 4
Length: 128441
Individuals with no LoFs: 125684
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125690
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.485	72	84.6	0.852	0.00000374	1029
Missense (PolyPhen)		21	38.951	0.53914		528
Synonymous	-0.167	33	31.8	1.04	0.00000142	310
Loss of Function	1.21	4	7.59	0.527	3.22e-7	95

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00014	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Positive regulator of amino acid starvation-induced autophagy. {ECO:0000269|PubMed:22354037}.;

Recessive Scores

pRec: 0.112

Intolerance Scores

LoFtool: 0.334
RVIS EVS: 0.7
RVIS percentile EVS: 85.34

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.499

Gene Damage Prediction

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