SRGN

serglycin, the group of Proteoglycans

Basic information

Region (hg38): 10:69088102-69104805

Previous symbols: [ "PRG", "PRG1" ]

Links

ENSG00000122862 ∙ NCBI:5552 ∙ OMIM:177040 ∙ HGNC:9361 ∙ Uniprot:P10124 ∙ 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 SRGN gene.

• not provided (3 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

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

Variants in SRGN

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

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

Position	Type	Phenotype	Significance	ClinVar
10-69088186-G-A		not specified	Uncertain significance (Jan 24, 2024)
10-69088188-C-T		not specified	Uncertain significance (Oct 17, 2023)
10-69097207-C-G			Benign (Jul 26, 2018)
10-69097209-C-A		not specified	Uncertain significance (Feb 27, 2024)
10-69103892-G-C		not specified	Uncertain significance (Jun 26, 2023)
10-69103897-G-A		not specified	Uncertain significance (Nov 07, 2023)
10-69103942-C-T			Benign (Jul 26, 2018)
10-69103944-G-A		not specified	Uncertain significance (Jun 09, 2022)
10-69103949-C-T			Benign/Likely benign (Apr 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SRGN	protein_coding	protein_coding	ENST00000242465	3	16706

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.697	0.288	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.596	76	92.1	0.825	0.00000530	1026
Missense in Polyphen		19	24.924	0.76232		317
Synonymous	0.958	28	35.2	0.795	0.00000199	315
Loss of Function	1.83	0	3.91	0.00	1.66e-7	46

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in formation of mast cell secretory granules and mediates storage of various compounds in secretory vesicles. Required for storage of some proteases in both connective tissue and mucosal mast cells and for storage of granzyme B in T-lymphocytes. Plays a role in localizing neutrophil elastase in azurophil granules of neutrophils. Mediates processing of MMP2. Plays a role in cytotoxic cell granule-mediated apoptosis by forming a complex with granzyme B which is delivered to cells by perforin to induce apoptosis. Regulates the secretion of TNF- alpha and may also regulate protease secretion. Inhibits bone mineralization. {ECO:0000269|PubMed:11911826, ECO:0000269|PubMed:16420477, ECO:0000269|PubMed:16870619}.
• Pathway: Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.216

Intolerance Scores

• loftool: 0.407
• rvis_EVS: 0.7
• rvis_percentile_EVS: 85.42

Haploinsufficiency Scores

• pHI: 0.709
• hipred: N
• hipred_score: 0.296
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.489

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Srgn
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: platelet degranulation;granzyme-mediated apoptotic signaling pathway;protein processing;negative regulation of bone mineralization;biomineral tissue development;mast cell secretory granule organization;T cell secretory granule organization;maintenance of protease location in mast cell secretory granule;maintenance of granzyme B location in T cell secretory granule;negative regulation of cytokine secretion
• Cellular component: extracellular region;extracellular space;Golgi apparatus;platelet alpha granule lumen;mast cell granule
• Molecular function: protein binding