SPRYD4

SPRY domain containing 4

Basic information

Region (hg38): 12:56468578-56479708

Links

ENSG00000176422 ∙ NCBI:283377 ∙ ∙ HGNC:27468 ∙ Uniprot:Q8WW59 ∙ 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 SPRYD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPRYD4 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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			15	2	1	18
Total	0	0	18	2	1

Variants in SPRYD4

This is a list of pathogenic ClinVar variants found in the SPRYD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-56469059-G-A		not specified	Uncertain significance (Sep 27, 2021)
12-56469143-G-A		not specified	Uncertain significance (Nov 20, 2024)
12-56469312-G-A		not specified	Uncertain significance (Feb 15, 2023)
12-56469465-C-T		not specified	Uncertain significance (Jan 30, 2024)
12-56471555-G-A		not specified	Uncertain significance (Jun 22, 2021)
12-56471611-T-A		not specified	Uncertain significance (Mar 19, 2024)
12-56471836-C-T		not specified	Uncertain significance (May 31, 2023)
12-56473229-C-T		not specified	Uncertain significance (Nov 27, 2023)
12-56473266-G-A		not specified	Uncertain significance (Jun 02, 2023)
12-56473561-C-T		not specified	Uncertain significance (Nov 08, 2022)
12-56474590-A-C		not specified	Uncertain significance (May 16, 2024)
12-56474667-G-A			Likely benign (May 01, 2022)
12-56474684-C-T		not specified	Uncertain significance (Jun 11, 2021)
12-56474882-C-T			Benign (Mar 29, 2018)
12-56475067-C-T		not specified	Uncertain significance (Oct 18, 2021)
12-56475081-C-T		not specified	Uncertain significance (Jan 24, 2024)
12-56475108-A-T		not specified	Uncertain significance (Oct 03, 2024)
12-56475621-T-C			Likely benign (Apr 10, 2018)
12-56475643-T-C		not specified	Uncertain significance (Jun 29, 2023)
12-56475651-T-C		not specified	Uncertain significance (Sep 08, 2024)
12-56475655-C-T		not specified	Uncertain significance (May 25, 2022)
12-56477954-T-G		not specified	Uncertain significance (Sep 12, 2023)
12-56477955-G-C		not specified	Uncertain significance (Sep 12, 2023)
12-56478013-A-C		not specified	Uncertain significance (Jan 30, 2024)
12-56478028-A-G		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPRYD4	protein_coding	protein_coding	ENST00000338146	2	2463

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00791	0.799	125724	0	23	125747	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.809	95	120	0.792	0.00000654	1324
Missense in Polyphen		22	45.671	0.48171		516
Synonymous	0.117	46	47.0	0.978	0.00000231	438
Loss of Function	1.01	4	6.85	0.584	3.03e-7	80

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000318	0.000318
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000705	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.0721

Intolerance Scores

• loftool: 0.612
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.06

Haploinsufficiency Scores

• pHI: 0.0945
• hipred: N
• hipred_score: 0.335
• ghis: 0.382

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.242

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spryd4

Gene ontology

• Biological process: biological_process
• Cellular component: nucleus
• Molecular function: molecular_function