SPRYD3

SPRY domain containing 3

Basic information

Region (hg38): 12:53064316-53079404

Links

ENSG00000167778 ∙ NCBI:84926 ∙ ∙ HGNC:25920 ∙ Uniprot:Q8NCJ5 ∙ 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 SPRYD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPRYD3 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	20	0	0

Variants in SPRYD3

This is a list of pathogenic ClinVar variants found in the SPRYD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-53065853-A-T		not specified	Uncertain significance (Jan 20, 2025)
12-53065935-C-G		not specified	Uncertain significance (Nov 06, 2023)
12-53066360-T-C		not specified	Uncertain significance (Apr 25, 2023)
12-53066388-C-T		not specified	Uncertain significance (Apr 12, 2022)
12-53066438-C-G		not specified	Uncertain significance (Jul 05, 2023)
12-53066590-T-C		not specified	Uncertain significance (Jan 03, 2024)
12-53068228-C-T		not specified	Uncertain significance (Apr 04, 2023)
12-53068229-G-A		not specified	Uncertain significance (Jul 31, 2023)
12-53068256-C-T		not specified	Uncertain significance (Oct 03, 2023)
12-53073298-T-A		not specified	Uncertain significance (Jan 23, 2025)
12-53073317-C-A		not specified	Uncertain significance (Feb 28, 2024)
12-53073317-C-T		not specified	Uncertain significance (May 24, 2024)
12-53073333-A-C		not specified	Uncertain significance (Mar 05, 2025)
12-53073365-C-T		not specified	Uncertain significance (Sep 01, 2024)
12-53073393-G-A		not specified	Uncertain significance (Dec 21, 2024)
12-53073441-C-T		not specified	Uncertain significance (May 09, 2022)
12-53074759-G-A		not specified	Uncertain significance (May 29, 2024)
12-53074777-T-C		not specified	Uncertain significance (Sep 11, 2024)
12-53075777-C-T		not specified	Uncertain significance (Nov 11, 2024)
12-53075806-T-C		not specified	Uncertain significance (Aug 11, 2022)
12-53077181-C-T		not specified	Uncertain significance (May 18, 2023)
12-53077261-C-A		not specified	Likely benign (Oct 07, 2024)
12-53079312-G-C		not specified	Uncertain significance (Nov 19, 2024)
12-53079320-C-A		not specified	Uncertain significance (Jul 19, 2022)
12-53079325-C-G		not specified	Uncertain significance (Aug 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPRYD3	protein_coding	protein_coding	ENST00000301463	11	14817

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.150	0.850	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.35	167	277	0.603	0.0000169	2900
Missense in Polyphen		39	97.121	0.40156		965
Synonymous	0.846	90	101	0.893	0.00000562	851
Loss of Function	3.33	6	23.4	0.257	0.00000138	253

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000610	0.0000610
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0868

Intolerance Scores

• loftool: 0.201
• rvis_EVS: -0.52
• rvis_percentile_EVS: 21.2

Haploinsufficiency Scores

• pHI: 0.185
• hipred: Y
• hipred_score: 0.617
• ghis: 0.592

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.955

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spryd3
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)