SPRN

shadow of prion protein

Basic information

Region (hg38): 10:133420666-133424625

Links

ENSG00000203772 ∙ NCBI:503542 ∙ OMIM:610447 ∙ HGNC:16871 ∙ Uniprot:Q5BIV9 ∙ 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 SPRN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPRN 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			40	2		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	2	0

Variants in SPRN

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

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

Position	Type	Phenotype	Significance	ClinVar
10-133423233-C-T		not specified	Uncertain significance (Sep 12, 2023)
10-133423264-C-T		not specified	Uncertain significance (Aug 27, 2024)
10-133423288-C-T		not specified	Likely benign (Jan 26, 2022)
10-133423290-C-A		not specified	Uncertain significance (Aug 04, 2024)
10-133423299-C-T		not specified	Uncertain significance (Jan 03, 2025)
10-133423314-C-G		not specified	Uncertain significance (Jun 09, 2022)
10-133423315-A-G		not specified	Uncertain significance (Jul 21, 2021)
10-133423351-T-G		not specified	Uncertain significance (Jan 26, 2022)
10-133423375-C-T		not specified	Uncertain significance (Sep 23, 2023)
10-133423395-C-T		not specified	Uncertain significance (Feb 05, 2024)
10-133423401-C-G		not specified	Uncertain significance (Sep 06, 2022)
10-133423413-C-T		not specified	Uncertain significance (Jan 26, 2022)
10-133423440-G-A		not specified	Uncertain significance (Feb 15, 2023)
10-133423446-G-A		not specified	Uncertain significance (Dec 16, 2022)
10-133423452-G-A		not specified	Uncertain significance (May 31, 2023)
10-133423461-C-A		not specified	Uncertain significance (Jul 14, 2023)
10-133423461-C-G		not specified	Uncertain significance (Aug 28, 2024)
10-133423473-C-G		not specified	Uncertain significance (Nov 03, 2023)
10-133423474-C-G		not specified	Uncertain significance (Sep 08, 2024)
10-133423474-C-T		not specified	Uncertain significance (Jun 19, 2024)
10-133423477-C-G		not specified	Uncertain significance (Feb 03, 2022)
10-133423479-G-A		not specified	Uncertain significance (Nov 13, 2024)
10-133423483-C-T		not specified	Uncertain significance (May 25, 2023)
10-133423503-G-A		not specified	Uncertain significance (Jul 14, 2024)
10-133423504-G-C		not specified	Uncertain significance (Feb 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPRN	protein_coding	protein_coding	ENST00000541506	1	148747

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.294	0.501	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.90	80	44.4	1.80	0.00000221	849
Missense in Polyphen		16	9.2848	1.7232		145
Synonymous	-3.40	41	21.1	1.94	0.00000111	363
Loss of Function	0.328	0	0.125	0.00	5.49e-9	1

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: Prion-like protein that has PrP(C)-like neuroprotective activity. May act as a modulator for the biological actions of normal and abnormal PrP (By similarity). {ECO:0000250}.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Haploinsufficiency Scores

• pHI: 0.0503
• hipred: N
• hipred_score: 0.367

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sprn
• Phenotype: growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: protein import into nucleus
• Cellular component: extracellular region;nucleus;nucleolus;cytosol;plasma membrane;anchored component of membrane;vesicle
• Molecular function: nucleic acid binding