SPRYD7

SPRY domain containing 7

Basic information

Region (hg38): 13:49912702-49936490

Previous symbols: [ "C13orf1" ]

Links

ENSG00000123178 ∙ NCBI:57213 ∙ OMIM:607866 ∙ HGNC:14297 ∙ Uniprot:Q5W111 ∙ 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 SPRYD7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPRYD7 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in SPRYD7

This is a list of pathogenic ClinVar variants found in the SPRYD7 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-49915104-G-A		not specified	Uncertain significance (Jun 22, 2023)
13-49921504-C-T		not specified	Uncertain significance (Jun 23, 2023)
13-49921508-T-C		not specified	Uncertain significance (Feb 03, 2022)
13-49921559-C-T		not specified	Uncertain significance (Aug 28, 2024)
13-49921579-C-A		not specified	Uncertain significance (May 31, 2023)
13-49927986-A-G		not specified	Uncertain significance (Mar 04, 2024)
13-49928038-T-C		not specified	Uncertain significance (Nov 11, 2024)
13-49928083-T-C		not specified	Uncertain significance (Mar 25, 2024)
13-49931134-C-T		not specified	Uncertain significance (Oct 06, 2022)
13-49936204-C-T		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPRYD7	protein_coding	protein_coding	ENST00000361840	5	23785

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000209	0.749	125732	0	15	125747	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.33	66	104	0.634	0.00000481	1285
Missense in Polyphen		17	30.549	0.55648		402
Synonymous	1.42	27	38.1	0.708	0.00000199	353
Loss of Function	1.01	7	10.5	0.664	6.28e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000126	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000551	0.0000544
Finnish	0.0000511	0.0000462
European (Non-Finnish)	0.0000804	0.0000791
Middle Eastern	0.0000551	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Intolerance Scores

• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.390
• ghis: 0.613

Essentials

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

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Spryd7

Gene ontology

• Molecular function: protein binding