SRPX

sushi repeat containing protein X-linked, the group of Sushi domain containing

Basic information

Region (hg38): X:38149336-38220924

Links

ENSG00000101955 ∙ NCBI:8406 ∙ OMIM:300187 ∙ HGNC:11309 ∙ Uniprot:P78539 ∙ 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 SRPX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRPX 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				3	1	4
missense			30		1	31
nonsense						0
start loss						0
frameshift						0
inframe indel			1	1		2
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	31	4	2

Variants in SRPX

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

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

Position	Type	Phenotype	Significance	ClinVar
X-38149849-C-A			Likely benign (Jun 04, 2018)
X-38149866-A-G		not specified	Uncertain significance (Dec 19, 2022)
X-38154473-C-T			Benign (Jun 13, 2018)
X-38154490-T-G		not specified	Uncertain significance (May 24, 2023)
X-38154494-C-G		not specified	Uncertain significance (Feb 07, 2023)
X-38154507-C-A		not specified	Uncertain significance (Dec 14, 2023)
X-38154523-G-A		not specified	Uncertain significance (Sep 12, 2023)
X-38154544-C-A		not specified	Uncertain significance (Feb 23, 2023)
X-38154558-C-A		not specified	Uncertain significance (Dec 26, 2023)
X-38154562-G-A		not specified	Uncertain significance (Mar 28, 2022)
X-38154583-G-T		not specified	Uncertain significance (Sep 16, 2021)
X-38156953-A-G			Likely benign (Aug 01, 2018)
X-38160034-G-A		not specified	Conflicting classifications of pathogenicity (Feb 01, 2023)
X-38160040-G-C		not specified	Uncertain significance (Apr 30, 2024)
X-38160076-C-A		not specified	Uncertain significance (Aug 26, 2022)
X-38160138-G-A			Likely benign (May 01, 2022)
X-38160141-G-T		not specified	Uncertain significance (Jan 23, 2024)
X-38160151-T-A		not specified	Uncertain significance (Dec 03, 2021)
X-38160935-C-A		not specified	Uncertain significance (Nov 17, 2023)
X-38160939-C-G		not specified	Uncertain significance (Jan 27, 2022)
X-38160947-C-G		not specified	Uncertain significance (Jan 17, 2024)
X-38160972-C-G		not specified	Uncertain significance (Oct 12, 2022)
X-38160977-C-G		Short stature	Likely pathogenic (Nov 18, 2001)
X-38160997-G-C		not specified	Uncertain significance (Jan 04, 2024)
X-38161032-G-C		not specified	Uncertain significance (Jun 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SRPX	protein_coding	protein_coding	ENST00000378533	10	72108

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00308	0.987	125725	9	5	125739	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.617	202	179	1.13	0.0000144	2960
Missense in Polyphen		84	80.878	1.0386		1381
Synonymous	-0.168	75	73.2	1.02	0.00000608	961
Loss of Function	2.25	7	17.0	0.412	0.00000152	274

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000760	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000136	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.000166	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in phagocytosis during disk shedding, cell adhesion to cells other than the pigment epithelium or signal transduction.

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.882
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.38

Haploinsufficiency Scores

• pHI: 0.638
• hipred: N
• hipred_score: 0.324
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Srpx
• Phenotype: neoplasm; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: phagolysosome assembly;autophagy;cell adhesion;response to endoplasmic reticulum stress;negative regulation of cell proliferation involved in contact inhibition;positive regulation of extrinsic apoptotic signaling pathway in absence of ligand
• Cellular component: autophagosome;endoplasmic reticulum;cell surface;membrane
• Molecular function: protein binding