SH2D4B

SH2 domain containing 4B, the group of SH2 domain containing

Basic information

Region (hg38): 10:80537901-80646560

Links

ENSG00000178217 ∙ NCBI:387694 ∙ ∙ HGNC:31440 ∙ Uniprot:Q5SQS7 ∙ 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 SH2D4B gene.

• Inborn genetic diseases (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH2D4B 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			1			1
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in SH2D4B

This is a list of pathogenic ClinVar variants found in the SH2D4B region.

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

Position	Type	Phenotype	Significance	ClinVar
10-80538374-C-G		not specified	Uncertain significance (Aug 16, 2022)
10-80538392-G-A		not specified	Uncertain significance (Jan 04, 2024)
10-80538425-C-T		not specified	Uncertain significance (Feb 16, 2023)
10-80538456-G-A		not specified	Uncertain significance (Jul 13, 2022)
10-80538471-C-A		not specified	Uncertain significance (Jul 13, 2022)
10-80538491-C-T		not specified	Uncertain significance (Oct 14, 2023)
10-80570280-C-T		not specified	Uncertain significance (Jul 27, 2022)
10-80571468-G-T		not specified	Uncertain significance (Jun 26, 2023)
10-80588639-G-A		not specified	Uncertain significance (Feb 11, 2022)
10-80588760-G-A		not specified	Uncertain significance (Jun 21, 2023)
10-80603585-G-A		not specified	Uncertain significance (Aug 12, 2021)
10-80603593-G-A		not specified	Uncertain significance (Oct 16, 2023)
10-80603639-A-G		not specified	Uncertain significance (Dec 14, 2021)
10-80603649-C-A		not specified	Uncertain significance (Feb 05, 2024)
10-80603660-G-A		not specified	Uncertain significance (Nov 10, 2022)
10-80603665-A-G		not specified	Uncertain significance (Nov 07, 2023)
10-80603665-A-T		not specified	Uncertain significance (Jul 14, 2021)
10-80603678-C-T		not specified	Uncertain significance (Oct 06, 2021)
10-80603704-C-T		not specified	Uncertain significance (Sep 22, 2022)
10-80603708-A-T		not specified	Uncertain significance (May 01, 2023)
10-80603762-C-T		not specified	Uncertain significance (Jan 18, 2022)
10-80609468-T-C		not specified	Uncertain significance (Dec 14, 2021)
10-80609469-C-G		not specified	Uncertain significance (Aug 02, 2021)
10-80609514-C-G		not specified	Uncertain significance (Jan 23, 2024)
10-80643996-G-A		not specified	Uncertain significance (Oct 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH2D4B	protein_coding	protein_coding	ENST00000339284	7	108659

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000634	0.975	125687	0	61	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0963	207	211	0.981	0.0000137	2286
Missense in Polyphen		56	63.798	0.87777		731
Synonymous	1.04	70	82.0	0.854	0.00000522	660
Loss of Function	2.06	12	22.5	0.533	0.00000139	216

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000645	0.000635
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000307	0.000273
Middle Eastern	0.00	0.00
South Asian	0.000525	0.000523
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.954
• rvis_EVS: 1.33
• rvis_percentile_EVS: 94.21

Haploinsufficiency Scores

• pHI: 0.347
• hipred: N
• hipred_score: 0.251

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.153

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh2d4b

Gene ontology

• Cellular component: cytoplasm