SCIN

scinderin, the group of Gelsolin/villins

Basic information

Region (hg38): 7:12570577-12660182

Links

ENSG00000006747 ∙ NCBI:85477 ∙ OMIM:613416 ∙ HGNC:21695 ∙ Uniprot:Q9Y6U3 ∙ 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 SCIN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCIN 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			58	3		61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	58	3	0

Variants in SCIN

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

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

Position	Type	Phenotype	Significance	ClinVar
7-12570791-C-T		not specified	Uncertain significance (Oct 10, 2023)
7-12570794-G-T		not specified	Uncertain significance (Apr 22, 2024)
7-12570824-C-T		not specified	Uncertain significance (Aug 30, 2021)
7-12570857-T-C		not specified	Uncertain significance (Jan 23, 2024)
7-12570874-G-T		not specified	Uncertain significance (Mar 19, 2024)
7-12570895-C-G		not specified	Uncertain significance (Mar 31, 2024)
7-12570947-C-T		not specified	Uncertain significance (Jan 23, 2023)
7-12570970-C-A		not specified	Uncertain significance (Sep 14, 2022)
7-12578105-T-G		not specified	Uncertain significance (Nov 21, 2024)
7-12578117-A-G		not specified	Uncertain significance (Sep 02, 2024)
7-12578204-G-A		not specified	Uncertain significance (Nov 18, 2022)
7-12581060-G-T		not specified	Uncertain significance (Dec 07, 2024)
7-12581097-C-T		not specified	Uncertain significance (Apr 06, 2023)
7-12581112-C-T		not specified	Uncertain significance (Dec 15, 2023)
7-12581118-G-T		not specified	Uncertain significance (Feb 13, 2023)
7-12581163-T-A		not specified	Uncertain significance (Jul 05, 2023)
7-12581172-G-A		not specified	Uncertain significance (Feb 28, 2023)
7-12581190-A-C		not specified	Uncertain significance (Jul 13, 2021)
7-12581192-G-A		not specified	Uncertain significance (May 28, 2024)
7-12581205-T-C		not specified	Uncertain significance (Oct 06, 2022)
7-12604521-A-G		not specified	Uncertain significance (May 21, 2024)
7-12604525-G-C		not specified	Uncertain significance (Jul 12, 2023)
7-12604556-C-T		not specified	Uncertain significance (Nov 10, 2022)
7-12604577-G-A		not specified	Uncertain significance (Sep 26, 2023)
7-12604587-T-G		not specified	Uncertain significance (Nov 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCIN	protein_coding	protein_coding	ENST00000297029	16	83026

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.72e-36	7.71e-8	124497	0	141	124638	0.000566

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.771	404	363	1.11	0.0000183	4645
Missense in Polyphen		172	157.05	1.0952		1957
Synonymous	-2.13	168	136	1.23	0.00000717	1326
Loss of Function	-1.71	48	36.8	1.30	0.00000173	474

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00158	0.00143
Ashkenazi Jewish	0.00	0.00
East Asian	0.000282	0.000278
Finnish	0.000326	0.000325
European (Non-Finnish)	0.000555	0.000540
Middle Eastern	0.000282	0.000278
South Asian	0.00100	0.000981
Other	0.000520	0.000496

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ca(2+)-dependent actin filament-severing protein that has a regulatory function in exocytosis by affecting the organization of the microfilament network underneath the plasma membrane (PubMed:8547642, PubMed:26365202). Severing activity is inhibited by phosphatidylinositol 4,5-bis-phosphate (PIP2) (By similarity). In vitro, also has barbed end capping and nucleating activities in the presence of Ca(2+). Required for megakaryocyte differentiation, maturation, polyploidization and apoptosis with the release of platelet-like particles (PubMed:11568009). Plays a role in osteoclastogenesis (OCG) and actin cytoskeletal organization in osteoclasts (By similarity). Regulates chondrocyte proliferation and differentiation (By similarity). Inhibits cell proliferation and tumorigenesis. Signaling is mediated by MAPK, p38 and JNK pathways (PubMed:11568009). {ECO:0000250|UniProtKB:Q28046, ECO:0000250|UniProtKB:Q5ZIV9, ECO:0000250|UniProtKB:Q60604, ECO:0000269|PubMed:11568009, ECO:0000269|PubMed:26365202, ECO:0000269|PubMed:8547642}.
• Pathway: Fc gamma R-mediated phagocytosis - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Endochondral Ossification (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.993
• rvis_EVS: 1.22
• rvis_percentile_EVS: 93.24

Haploinsufficiency Scores

• pHI: 0.497
• hipred: N
• hipred_score: 0.449

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.714

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scin
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; skeleton phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: negative regulation of cell population proliferation;calcium ion regulated exocytosis;regulation of chondrocyte differentiation;sequestering of actin monomers;positive regulation of apoptotic process;actin nucleation;positive regulation of megakaryocyte differentiation;actin filament severing;positive regulation of secretion;positive regulation of actin nucleation;actin filament capping
• Cellular component: podosome;cytoplasm;plasma membrane;brush border;cell cortex;cell junction;cell projection;extracellular exosome
• Molecular function: phosphatidylserine binding;actin binding;calcium ion binding;1-phosphatidylinositol binding;phosphatidylinositol-4,5-bisphosphate binding;actin filament binding