SCOC

short coiled-coil protein

Basic information

Region (hg38): 4:140257285-140385728

Links

ENSG00000153130 ∙ NCBI:60592 ∙ ∙ HGNC:20335 ∙ Uniprot:Q9UIL1 ∙ 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 SCOC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCOC 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			2			2
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			6	1	1	8
Total	0	0	9	1	1

Variants in SCOC

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

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

Position	Type	Phenotype	Significance	ClinVar
4-140343661-A-C		not specified	Uncertain significance (Aug 02, 2021)
4-140373589-G-C		not specified	Uncertain significance (Jan 24, 2023)
4-140373606-C-T		not specified	Uncertain significance (Sep 01, 2021)
4-140373633-C-G		not specified	Uncertain significance (Dec 28, 2022)
4-140373640-G-C		not specified	Uncertain significance (Jan 24, 2023)
4-140373669-C-A		not specified	Uncertain significance (Aug 04, 2023)
4-140373681-G-T		not specified	Likely benign (Sep 22, 2022)
4-140373688-C-T		not specified	Uncertain significance (May 18, 2023)
4-140373726-C-A			Benign (Mar 29, 2018)
4-140379171-A-G		not specified	Uncertain significance (Nov 23, 2021)
4-140379581-A-C		not specified	Uncertain significance (Dec 12, 2023)
4-140379634-C-A		not specified	Uncertain significance (Jul 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCOC	protein_coding	protein_coding	ENST00000608372	4	128441

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0111	0.851	125684	0	6	125690	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.485	72	84.6	0.852	0.00000374	1029
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000143	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000179	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Positive regulator of amino acid starvation-induced autophagy. {ECO:0000269|PubMed:22354037}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.334
• rvis_EVS: 0.7
• rvis_percentile_EVS: 85.34

Haploinsufficiency Scores

• pHI: 0.300
• hipred: N
• hipred_score: 0.171
• ghis: 0.703

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.499

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scoc

Gene ontology

• Biological process: positive regulation of macroautophagy;regulation of protein complex stability
• Cellular component: Golgi membrane;nucleoplasm;endosome;Golgi apparatus;trans-Golgi network;cytosol
• Molecular function: protein binding