SH3PXD2A

SH3 and PX domains 2A

Basic information

Region (hg38): 10:103594026-103855584

Previous symbols: [ "SH3MD1" ]

Links

ENSG00000107957 ∙ NCBI:9644 ∙ OMIM:619455 ∙ HGNC:23664 ∙ Uniprot:Q5TCZ1 ∙ 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 SH3PXD2A gene.

• Inborn genetic diseases (53 variants)
• not provided (6 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH3PXD2A 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					2	2
missense			50	4	3	57
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	50	4	5

Variants in SH3PXD2A

This is a list of pathogenic ClinVar variants found in the SH3PXD2A region.

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

Position	Type	Phenotype	Significance	ClinVar
10-103601838-T-G		not specified	Uncertain significance (Aug 01, 2022)
10-103601879-G-C		not specified	Uncertain significance (Jan 24, 2024)
10-103601986-C-T		not specified	Uncertain significance (Jan 18, 2023)
10-103602013-T-G		not specified	Uncertain significance (Dec 19, 2023)
10-103602018-T-C		not specified	Uncertain significance (Dec 21, 2022)
10-103602055-C-A		not specified	Uncertain significance (Dec 02, 2022)
10-103602055-C-T		not specified	Uncertain significance (Apr 07, 2023)
10-103602075-G-A		not specified	Uncertain significance (Jan 03, 2024)
10-103602114-C-T			Benign (Nov 10, 2017)
10-103602126-C-T		not specified	Uncertain significance (Feb 03, 2022)
10-103602141-G-A		not specified	Uncertain significance (May 10, 2022)
10-103602142-C-T		not specified	Uncertain significance (Jun 27, 2022)
10-103602148-C-T		not specified	Uncertain significance (Jul 12, 2023)
10-103602153-C-T		not specified	Uncertain significance (Sep 01, 2021)
10-103602154-G-A			Likely benign (Jun 06, 2018)
10-103602184-C-T			Benign (Dec 31, 2019)
10-103602225-C-T		not specified	Uncertain significance (Jan 24, 2024)
10-103602261-G-A		not specified	Uncertain significance (Mar 01, 2024)
10-103602276-G-A		not specified	Uncertain significance (May 04, 2023)
10-103602291-G-A		not specified	Uncertain significance (Jan 03, 2024)
10-103602294-A-G		not specified	Uncertain significance (Oct 26, 2022)
10-103602314-C-T		not specified	Uncertain significance (Feb 22, 2024)
10-103602355-C-T		not specified	Uncertain significance (Apr 28, 2023)
10-103602380-C-T			Benign (Jun 06, 2018)
10-103602385-C-T		not specified	Uncertain significance (Dec 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH3PXD2A	protein_coding	protein_coding	ENST00000355946	14	267017

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.989	0.0110	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.56	561	675	0.831	0.0000435	7112
Missense in Polyphen		260	344.45	0.75482		3632
Synonymous	0.294	292	298	0.978	0.0000209	2265
Loss of Function	5.42	8	48.8	0.164	0.00000243	557

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000254	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000129	0.0000924
European (Non-Finnish)	0.0000746	0.0000615
Middle Eastern	0.000163	0.000163
South Asian	0.0000369	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adapter protein involved in invadopodia and podosome formation, extracellular matrix degradation and invasiveness of some cancer cells. Binds matrix metalloproteinases (ADAMs), NADPH oxidases (NOXs) and phosphoinositides. Acts as an organizer protein that allows NOX1- or NOX3-dependent reactive oxygen species (ROS) generation and ROS localization. In association with ADAM12, mediates the neurotoxic effect of amyloid-beta peptide. {ECO:0000269|PubMed:12615925, ECO:0000269|PubMed:15710328, ECO:0000269|PubMed:15710903, ECO:0000269|PubMed:19755710, ECO:0000269|PubMed:20609497}.
• Pathway: Invadopodia formation;Extracellular matrix organization (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.386
• rvis_EVS: -1.83
• rvis_percentile_EVS: 2.12

Haploinsufficiency Scores

• pHI: 0.442
• hipred: Y
• hipred_score: 0.694
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.751

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh3pxd2a
• Phenotype: hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); liver/biliary system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; skeleton phenotype; renal/urinary system phenotype; immune system phenotype; vision/eye phenotype; digestive/alimentary phenotype; muscle phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; craniofacial phenotype

Zebrafish Information Network

• Gene name: sh3pxd2aa
• Affected structure: neural crest cell
• Phenotype tag: abnormal
• Phenotype quality: increased amount

Gene ontology

• Biological process: superoxide metabolic process;extracellular matrix organization;positive regulation of catalytic activity;osteoclast fusion
• Cellular component: podosome;cytosol;cell junction;cell projection
• Molecular function: protease binding;protein binding;phosphatidylinositol-4,5-bisphosphate binding;phosphatidylinositol-5-phosphate binding;superoxide-generating NADPH oxidase activator activity;phosphatidylinositol-3-phosphate binding;phosphatidylinositol binding;phosphatidylinositol-3,4-bisphosphate binding;phosphatidylinositol-4-phosphate binding