SH2D7

SH2 domain containing 7, the group of SH2 domain containing

Basic information

Region (hg38): 15:78077808-78104370

Links

ENSG00000183476 ∙ NCBI:646892 ∙ ∙ HGNC:34549 ∙ Uniprot:A6NKC9 ∙ 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 SH2D7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH2D7 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			33	4		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	4	0

Variants in SH2D7

This is a list of pathogenic ClinVar variants found in the SH2D7 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-78092629-G-C		not specified	Uncertain significance (Jan 29, 2024)
15-78092684-T-G		not specified	Uncertain significance (Jun 30, 2022)
15-78094117-C-T		not specified	Uncertain significance (Nov 11, 2024)
15-78094141-C-T		not specified	Uncertain significance (Oct 06, 2021)
15-78094174-G-A		not specified	Uncertain significance (Feb 23, 2023)
15-78094198-A-G		not specified	Uncertain significance (May 26, 2024)
15-78097940-G-A		not specified	Uncertain significance (Oct 20, 2023)
15-78097951-T-C		not specified	Uncertain significance (Sep 20, 2023)
15-78097960-A-G		not specified	Uncertain significance (Apr 28, 2023)
15-78097978-C-T		not specified	Uncertain significance (Oct 05, 2023)
15-78097997-A-G		not specified	Uncertain significance (Jan 04, 2024)
15-78098051-A-G		not specified	Uncertain significance (Oct 24, 2024)
15-78098069-A-G		not specified	Uncertain significance (Jan 02, 2024)
15-78098089-C-T		not specified	Uncertain significance (Nov 17, 2022)
15-78098090-C-A		not specified	Uncertain significance (Aug 17, 2022)
15-78098463-C-T		not specified	Likely benign (Feb 15, 2023)
15-78098495-G-A		not specified	Uncertain significance (Jun 05, 2023)
15-78098496-C-T		not specified	Uncertain significance (Oct 17, 2023)
15-78098504-C-T		not specified	Likely benign (Jul 25, 2023)
15-78098505-G-A		not specified	Uncertain significance (Jul 25, 2023)
15-78098517-A-C		not specified	Uncertain significance (Jun 03, 2022)
15-78098544-A-G		not specified	Uncertain significance (Jun 21, 2022)
15-78098548-A-T		not specified	Uncertain significance (Jul 20, 2021)
15-78098568-G-A		not specified	Uncertain significance (Mar 20, 2023)
15-78098587-A-C		not specified	Uncertain significance (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH2D7	protein_coding	protein_coding	ENST00000328828	6	27102

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.37e-8	0.473	124525	1	106	124632	0.000429

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.102	243	248	0.982	0.0000135	2895
Missense in Polyphen		29	35.373	0.81984		441
Synonymous	0.405	92	97.1	0.948	0.00000506	914
Loss of Function	0.939	14	18.3	0.763	0.00000102	188

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000293	0.000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00474	0.00468
Finnish	0.00	0.00
European (Non-Finnish)	0.0000379	0.0000354
Middle Eastern	0.00474	0.00468
South Asian	0.000276	0.000261
Other	0.000665	0.000661

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.625
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.54

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0216

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh2d7

Gene ontology

• Cellular component: cytoplasm