SH2D3A

SH2 domain containing 3A, the group of NSP adaptor proteins|SH2 domain containing

Basic information

Region (hg38): 19:6752159-6767463

Links

ENSG00000125731 ∙ NCBI:10045 ∙ OMIM:604721 ∙ HGNC:16885 ∙ Uniprot:Q9BRG2 ∙ 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 SH2D3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH2D3A 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			35			35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	0	0

Variants in SH2D3A

This is a list of pathogenic ClinVar variants found in the SH2D3A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-6752634-C-G		not specified	Uncertain significance (Mar 29, 2023)
19-6752682-G-A		not specified	Uncertain significance (Jan 16, 2024)
19-6752694-G-C		not specified	Uncertain significance (Jun 03, 2022)
19-6752702-C-T		not specified	Uncertain significance (Nov 09, 2022)
19-6753530-C-G		not specified	Uncertain significance (Jan 29, 2024)
19-6753539-C-G		not specified	Uncertain significance (Sep 13, 2023)
19-6753540-G-A		not specified	Uncertain significance (Apr 18, 2024)
19-6753552-C-G		not specified	Uncertain significance (Sep 21, 2023)
19-6754133-G-A		not specified	Uncertain significance (Dec 28, 2022)
19-6754139-G-C		not specified	Uncertain significance (Dec 17, 2021)
19-6754274-T-C		not specified	Uncertain significance (Jul 13, 2022)
19-6754303-G-C		not specified	Uncertain significance (Dec 28, 2022)
19-6754390-A-G		not specified	Uncertain significance (Mar 31, 2024)
19-6754698-G-A		not specified	Uncertain significance (Jul 06, 2021)
19-6754716-C-T		not specified	Uncertain significance (May 13, 2024)
19-6754864-G-T		not specified	Uncertain significance (Oct 17, 2023)
19-6754925-G-A		not specified	Uncertain significance (Mar 09, 2022)
19-6754967-G-A		not specified	Uncertain significance (Jan 17, 2023)
19-6754988-T-G		not specified	Uncertain significance (Jul 12, 2022)
19-6755028-C-T		not specified	Uncertain significance (Feb 05, 2024)
19-6755253-C-A		not specified	Uncertain significance (Aug 01, 2022)
19-6759665-C-G		not specified	Uncertain significance (May 02, 2024)
19-6760644-G-C		not specified	Uncertain significance (Mar 09, 2022)
19-6760659-G-A		not specified	Uncertain significance (Jan 04, 2024)
19-6760668-A-T		not specified	Uncertain significance (Oct 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH2D3A	protein_coding	protein_coding	ENST00000245908	9	15429

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.64e-8	0.795	125486	0	262	125748	0.00104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	310	366	0.846	0.0000245	3587
Missense in Polyphen		103	110.69	0.93051		1224
Synonymous	1.15	141	160	0.884	0.0000103	1293
Loss of Function	1.47	15	22.5	0.667	0.00000130	224

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00328	0.00327
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.00365	0.00365
Finnish	0.000716	0.000462
European (Non-Finnish)	0.000570	0.000563
Middle Eastern	0.00365	0.00365
South Asian	0.00157	0.00157
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in JNK activation.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.554
• rvis_EVS: 1.51
• rvis_percentile_EVS: 95.47

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.180
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.429

Gene Damage Prediction

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

Gene ontology

• Biological process: JNK cascade;small GTPase mediated signal transduction;positive regulation of signal transduction;positive regulation of peptidyl-serine phosphorylation
• Molecular function: SH3/SH2 adaptor activity;guanyl-nucleotide exchange factor activity;protein binding