SYNCRIP

synaptotagmin binding cytoplasmic RNA interacting protein, the group of RNA binding motif containing|Heterogeneous nuclear ribonucleoproteins

Basic information

Region (hg38): 6:85607779-85644063

Links

ENSG00000135316 ∙ NCBI:10492 ∙ OMIM:616686 ∙ HGNC:16918 ∙ Uniprot:O60506 ∙ 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 SYNCRIP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYNCRIP 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				3	1	4
missense			30	1	1	32
nonsense			1			1
start loss						0
frameshift		2	2			4
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	2	34	4	2

Variants in SYNCRIP

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

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

Position	Type	Phenotype	Significance	ClinVar
6-85614764-A-G		SYNCRIP-related disorder	Uncertain significance (Apr 11, 2023)
6-85614765-C-A		Inborn genetic diseases	Uncertain significance (Jan 31, 2024)
6-85614779-T-A		Inborn genetic diseases	Uncertain significance (Mar 30, 2024)
6-85614793-T-A		Inborn genetic diseases	Likely benign (May 24, 2023)
6-85614805-G-C		Inborn genetic diseases	Uncertain significance (Dec 15, 2022)
6-85614817-T-C		Inborn genetic diseases	Benign (Jun 07, 2022)
6-85614820-T-G			Uncertain significance (Jul 22, 2024)
6-85614826-G-C			Uncertain significance (Mar 17, 2023)
6-85614840-T-C		SYNCRIP-related disorder	Likely benign (Sep 19, 2019)
6-85614852-C-T		SYNCRIP-related disorder	Likely benign (Mar 28, 2019)
6-85614876-G-C			Uncertain significance (Dec 29, 2023)
6-85614886-T-C		Inborn genetic diseases	Uncertain significance (Feb 09, 2022)
6-85614928-G-A		Inborn genetic diseases	Uncertain significance (Jun 17, 2024)
6-85614946-A-C		SYNCRIP-related disorder	Uncertain significance (Jan 11, 2023)
6-85614984-G-A		SYNCRIP-related disorder	Likely benign (Aug 14, 2019)
6-85614986-G-A			Uncertain significance (Jul 25, 2022)
6-85614988-C-A		Inborn genetic diseases	Uncertain significance (Aug 21, 2023)
6-85615007-C-A		Inborn genetic diseases	Uncertain significance (Sep 30, 2024)
6-85615025-C-T		Inborn genetic diseases	Uncertain significance (Nov 08, 2021)
6-85615054-TG-AA		Autism spectrum disorder	association (-)
6-85615058-A-C		Inborn genetic diseases	Uncertain significance (Mar 30, 2024)
6-85615059-ATAACC-A			Uncertain significance (Dec 10, 2023)
6-85615061-A-G		SYNCRIP-related disorder	Uncertain significance (Sep 28, 2024)
6-85615064-C-T		Inborn genetic diseases	Uncertain significance (Sep 16, 2021)
6-85615067-C-T		SYNCRIP-related Intellectual Disability	Uncertain significance (Jan 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYNCRIP	protein_coding	protein_coding	ENST00000369622	10	35458

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000612	125739	0	6	125745	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.54	163	349	0.467	0.0000188	4066
Missense in Polyphen		29	118.97	0.24375		1563
Synonymous	-0.886	128	116	1.10	0.00000620	1182
Loss of Function	4.75	2	30.1	0.0663	0.00000158	389

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Heterogenous nuclear ribonucleoprotein (hnRNP) implicated in mRNA processing mechanisms. Component of the CRD- mediated complex that promotes MYC mRNA stability. Isoform 1, isoform 2 and isoform 3 are associated in vitro with pre-mRNA, splicing intermediates and mature mRNA protein complexes. Isoform 1 binds to apoB mRNA AU-rich sequences. Isoform 1 is part of the APOB mRNA editosome complex and may modulate the postranscriptional C to U RNA-editing of the APOB mRNA through either by binding to A1CF (APOBEC1 complementation factor), to APOBEC1 or to RNA itself. May be involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Interacts in vitro preferentially with poly(A) and poly(U) RNA sequences. Isoform 3 may be involved in cytoplasmic vesicle-based mRNA transport through interaction with synaptotagmins. Component of the GAIT (gamma interferon-activated inhibitor of translation) complex which mediates interferon-gamma- induced transcript-selective translation inhibition in inflammation processes. Upon interferon-gamma activation assembles into the GAIT complex which binds to stem loop-containing GAIT elements in the 3'-UTR of diverse inflammatory mRNAs (such as ceruplasmin) and suppresses their translation; seems not to be essential for GAIT complex function. {ECO:0000269|PubMed:11051545, ECO:0000269|PubMed:11134005, ECO:0000269|PubMed:11352648, ECO:0000269|PubMed:11574476, ECO:0000269|PubMed:19029303, ECO:0000269|PubMed:23071094}.

Recessive Scores

• pRec: 0.250

Intolerance Scores

• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.31

Haploinsufficiency Scores

• pHI: 0.977
• hipred: Y
• hipred_score: 0.783
• ghis: 0.708

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syncrip

Gene ontology

• Biological process: mRNA splicing, via spliceosome;osteoblast differentiation;RNA processing;RNA splicing;viral process;negative regulation of translation;CRD-mediated mRNA stabilization;cellular response to interferon-gamma
• Cellular component: nucleus;nucleoplasm;endoplasmic reticulum;membrane;CRD-mediated mRNA stability complex;catalytic step 2 spliceosome;histone pre-mRNA 3'end processing complex;GAIT complex;ribonucleoprotein complex
• Molecular function: RNA binding;mRNA binding;protein binding;poly(A) binding;mRNA 5'-UTR binding