SH2D6

SH2 domain containing 6, the group of SH2 domain containing

Basic information

Region (hg38): 2:85418714-85437029

Links

ENSG00000152292 ∙ NCBI:284948 ∙ ∙ HGNC:30439 ∙ Uniprot:Q7Z4S9 ∙ 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 SH2D6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH2D6 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			14	3		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	2		3
Total	0	0	15	5	0

Variants in SH2D6

This is a list of pathogenic ClinVar variants found in the SH2D6 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-85434978-C-T		not specified	Likely benign (May 09, 2023)
2-85434984-C-T		not specified	Likely benign (Jan 21, 2025)
2-85434996-C-T		not specified	Uncertain significance (Nov 09, 2023)
2-85435014-C-T		not specified	Likely benign (Sep 28, 2022)
2-85435077-C-T		not specified	Uncertain significance (Feb 10, 2025)
2-85435121-G-A		not specified	Uncertain significance (Nov 20, 2023)
2-85435413-G-A		not specified	Uncertain significance (Mar 01, 2023)
2-85435458-C-T		not specified	Uncertain significance (Mar 15, 2024)
2-85435467-G-A		not specified	Uncertain significance (Jun 22, 2024)
2-85435684-C-T		not specified	Uncertain significance (Apr 23, 2024)
2-85435685-G-A		not specified	Uncertain significance (Aug 23, 2021)
2-85435714-C-T		not specified	Uncertain significance (Feb 11, 2022)
2-85435769-G-A		not specified	Likely benign (Mar 11, 2024)
2-85435784-G-A		not specified	Likely benign (Aug 28, 2023)
2-85435802-G-A		not specified	Uncertain significance (Sep 06, 2022)
2-85435808-G-A		not specified	Uncertain significance (Nov 27, 2024)
2-85435817-G-A		not specified	Likely benign (Feb 27, 2023)
2-85435822-G-A		not specified	Uncertain significance (Feb 15, 2023)
2-85436488-T-C		not specified	Uncertain significance (Sep 06, 2022)
2-85436504-G-A		not specified	Uncertain significance (Nov 20, 2023)
2-85436538-G-A		not specified	Uncertain significance (Sep 28, 2022)
2-85436544-C-T		not specified	Uncertain significance (Oct 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH2D6	protein_coding	protein_coding	ENST00000340326	4	18309

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000377	0.392	125698	0	36	125734	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.467	91	104	0.871	0.00000663	1083
Missense in Polyphen		27	32.086	0.84148		352
Synonymous	0.769	37	43.4	0.852	0.00000262	387
Loss of Function	0.229	7	7.69	0.911	4.10e-7	83

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00135	0.00135
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000536	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000982	0.0000980
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.519
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.28

Haploinsufficiency Scores

• pHI: 0.0582
• hipred: N
• hipred_score: 0.123
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0173

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh2d6

Gene ontology

• Biological process: transmembrane receptor protein tyrosine kinase signaling pathway;positive regulation of signal transduction;intracellular signal transduction
• Cellular component: cytoplasm
• Molecular function: SH3/SH2 adaptor activity