SH2D4A

SH2 domain containing 4A, the group of Protein phosphatase 1 regulatory subunits|SH2 domain containing

Basic information

Region (hg38): 8:19313692-19396218

Links

ENSG00000104611 ∙ NCBI:63898 ∙ OMIM:614968 ∙ HGNC:26102 ∙ Uniprot:Q9H788 ∙ 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 SH2D4A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH2D4A 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			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	0

Variants in SH2D4A

This is a list of pathogenic ClinVar variants found in the SH2D4A region.

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

Position	Type	Phenotype	Significance	ClinVar
8-19319579-T-C		not specified	Uncertain significance (Aug 02, 2023)
8-19332967-C-T		not specified	Uncertain significance (Nov 09, 2021)
8-19332972-C-A		not specified	Uncertain significance (Mar 20, 2023)
8-19334705-T-G		not specified	Uncertain significance (Apr 25, 2022)
8-19334754-C-T		not specified	Uncertain significance (May 04, 2022)
8-19357233-C-A		not specified	Uncertain significance (Jan 26, 2022)
8-19357251-A-G		not specified	Uncertain significance (Dec 19, 2022)
8-19357257-C-A		not specified	Uncertain significance (Dec 13, 2021)
8-19361276-G-C		not specified	Uncertain significance (May 23, 2024)
8-19361303-G-T		not specified	Uncertain significance (Nov 22, 2023)
8-19364075-G-A		not specified	Uncertain significance (May 26, 2023)
8-19364097-G-C		not specified	Uncertain significance (Sep 13, 2023)
8-19364104-C-T		not specified	Uncertain significance (Oct 10, 2023)
8-19364147-C-A		not specified	Uncertain significance (Aug 12, 2021)
8-19364152-G-A		not specified	Uncertain significance (Feb 15, 2024)
8-19364198-G-A		not specified	Uncertain significance (Aug 16, 2021)
8-19364204-C-T		not specified	Uncertain significance (May 16, 2024)
8-19364225-C-T		not specified	Uncertain significance (Sep 19, 2023)
8-19373543-G-A		not specified	Uncertain significance (May 15, 2024)
8-19373583-G-A		not specified	Uncertain significance (Jul 09, 2021)
8-19373613-G-A		not specified	Uncertain significance (Aug 02, 2021)
8-19393320-A-G		not specified	Uncertain significance (Dec 19, 2023)
8-19393329-C-T		not specified	Uncertain significance (Aug 13, 2021)
8-19393357-G-A		not specified	Uncertain significance (Dec 21, 2022)
8-19393380-C-A		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH2D4A	protein_coding	protein_coding	ENST00000265807	9	82602

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.14e-22	0.000544	125302	2	444	125748	0.00178

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.17	334	240	1.39	0.0000130	2958
Missense in Polyphen		103	70.297	1.4652		843
Synonymous	-2.59	125	93.2	1.34	0.00000546	826
Loss of Function	-0.276	32	30.4	1.05	0.00000198	310

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00161	0.00160
Ashkenazi Jewish	0.00123	0.00119
East Asian	0.00542	0.00534
Finnish	0.000418	0.000416
European (Non-Finnish)	0.00215	0.00211
Middle Eastern	0.00542	0.00534
South Asian	0.00122	0.00111
Other	0.00202	0.00179

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits estrogen-induced cell proliferation by competing with PLCG for binding to ESR1, blocking the effect of estrogen on PLCG and repressing estrogen-induced proliferation. May play a role in T-cell development and function. {ECO:0000269|PubMed:18641339, ECO:0000269|PubMed:19712589}.

Recessive Scores

• pRec: 0.0945

Intolerance Scores

• loftool: 0.629
• rvis_EVS: 0.69
• rvis_percentile_EVS: 85.24

Haploinsufficiency Scores

• pHI: 0.138
• hipred: N
• hipred_score: 0.170
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.788

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh2d4a
• Phenotype: normal phenotype

Gene ontology

• Biological process: negative regulation of phosphatase activity
• Cellular component: cytoplasm;cytosol
• Molecular function: protein binding;phosphatase binding