SYNC

syncoilin, intermediate filament protein, the group of Intermediate filaments Type III

Basic information

Region (hg38): 1:32679906-32703596

Previous symbols: [ "SYNC1" ]

Links

ENSG00000162520 ∙ NCBI:81493 ∙ OMIM:611750 ∙ HGNC:28897 ∙ Uniprot:Q9H7C4 ∙ 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 SYNC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYNC 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				1		1
missense			28	2		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	3	0

Variants in SYNC

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

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

Position	Type	Phenotype	Significance	ClinVar
1-32684061-G-C		not specified	Uncertain significance (Jan 26, 2022)
1-32684280-C-T		not specified	Uncertain significance (Aug 11, 2022)
1-32684324-T-C		not specified	Uncertain significance (Feb 23, 2023)
1-32694906-G-A		not specified	Uncertain significance (Jan 10, 2023)
1-32694918-C-T		not specified	Uncertain significance (Apr 15, 2024)
1-32694942-G-A		not specified	Uncertain significance (Jun 27, 2022)
1-32694951-G-A		not specified	Uncertain significance (Aug 01, 2024)
1-32694954-C-T		not specified	Uncertain significance (Feb 10, 2023)
1-32694965-A-G		not specified	Uncertain significance (Aug 01, 2024)
1-32695001-G-C		not specified	Uncertain significance (Feb 05, 2024)
1-32695086-C-T		SYNC-related disorder	Likely benign (Jan 12, 2023)
1-32695091-C-T		not specified	Uncertain significance (Mar 08, 2024)
1-32695129-T-C			Likely benign (Nov 01, 2024)
1-32695130-C-T		not specified	Uncertain significance (Jul 14, 2021)
1-32695137-T-C		not specified	Uncertain significance (Apr 26, 2024)
1-32695147-A-T		not specified	Uncertain significance (Oct 06, 2021)
1-32695190-C-T		not specified	Uncertain significance (Oct 12, 2021)
1-32695223-C-T		not specified	Uncertain significance (Aug 15, 2024)
1-32695296-C-T		not specified	Uncertain significance (Dec 28, 2023)
1-32695341-A-G		not specified	Uncertain significance (Jan 18, 2023)
1-32695472-T-C		not specified	Uncertain significance (Sep 04, 2024)
1-32695518-C-A		not specified	Uncertain significance (Oct 14, 2021)
1-32695525-C-G		not specified	Uncertain significance (Apr 26, 2024)
1-32695558-C-T			Likely benign (Jul 01, 2022)
1-32695565-C-G		not specified	Uncertain significance (Sep 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYNC	protein_coding	protein_coding	ENST00000409190	5	23691

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000186	0.974	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.668	216	245	0.880	0.0000132	3114
Missense in Polyphen		78	92.458	0.84363		1235
Synonymous	1.23	83	98.5	0.843	0.00000504	942
Loss of Function	2.02	11	21.0	0.524	0.00000109	246

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000487	0.000486
Ashkenazi Jewish	0.00	0.00
East Asian	0.000279	0.000272
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.000109	0.000105
Middle Eastern	0.000279	0.000272
South Asian	0.0000331	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Atypical type III intermediate filament (IF) protein that may play a supportive role in the efficient coupling of mechanical stress between the myofibril and fiber exterior. May facilitate lateral force transmission during skeletal muscle contraction. Does not form homofilaments nor heterofilaments with other IF proteins. {ECO:0000250|UniProtKB:Q9EPM5}.

Intolerance Scores

• loftool: 0.205
• rvis_EVS: 1.48
• rvis_percentile_EVS: 95.31

Haploinsufficiency Scores

• pHI: 0.810
• hipred: N
• hipred_score: 0.244

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0573

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sync
• Phenotype: muscle phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: intermediate filament-based process
• Cellular component: cytosol;intermediate filament;Z disc;neuromuscular junction;sarcolemma;perinuclear region of cytoplasm
• Molecular function: structural molecule activity