SHD

Src homology 2 domain containing transforming protein D, the group of SH2 domain containing

Basic information

Region (hg38): 19:4279266-4290722

Links

ENSG00000105251 ∙ NCBI:56961 ∙ OMIM:610481 ∙ HGNC:30633 ∙ Uniprot:Q96IW2 ∙ 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 SHD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHD 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			40	1		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	1	0

Variants in SHD

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

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

Position	Type	Phenotype	Significance	ClinVar
19-4280080-G-T		not specified	Uncertain significance (Jul 15, 2021)
19-4280101-G-A		not specified	Uncertain significance (Dec 07, 2022)
19-4280217-C-T		not specified	Uncertain significance (Dec 30, 2023)
19-4280218-G-T		not specified	Uncertain significance (Oct 18, 2021)
19-4280260-C-T		not specified	Uncertain significance (Nov 25, 2024)
19-4280265-G-C		not specified	Uncertain significance (Sep 22, 2023)
19-4280292-C-T		not specified	Uncertain significance (Aug 12, 2021)
19-4280310-G-T		not specified	Uncertain significance (Oct 26, 2021)
19-4282894-G-C		not specified	Uncertain significance (Aug 08, 2023)
19-4282928-C-T		not specified	Uncertain significance (Apr 21, 2022)
19-4282933-G-A		not specified	Uncertain significance (Apr 18, 2023)
19-4282936-G-A		not specified	Uncertain significance (Apr 07, 2023)
19-4282954-G-A		not specified	Uncertain significance (Aug 20, 2024)
19-4283059-C-A		not specified	Uncertain significance (Jun 13, 2024)
19-4283071-G-A		not specified	Uncertain significance (Apr 08, 2022)
19-4283101-C-A		not specified	Uncertain significance (Dec 22, 2023)
19-4283132-C-T		not specified	Uncertain significance (Mar 08, 2024)
19-4283146-C-T		not specified	Uncertain significance (Jan 22, 2025)
19-4283153-G-A		not specified	Uncertain significance (Aug 28, 2024)
19-4283154-C-G		not specified	Uncertain significance (Aug 09, 2021)
19-4283172-T-A		not specified	Uncertain significance (Jun 09, 2022)
19-4283173-G-C		not specified	Uncertain significance (Jan 31, 2024)
19-4283176-C-T		not specified	Uncertain significance (Aug 20, 2024)
19-4283234-C-T		not specified	Uncertain significance (Jul 22, 2024)
19-4284793-G-C		not specified	Uncertain significance (Nov 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHD	protein_coding	protein_coding	ENST00000543264	6	12124

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000836	0.772	125712	0	35	125747	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.432	229	211	1.08	0.0000121	2197
Missense in Polyphen		66	62.38	1.058		680
Synonymous	-0.714	100	91.3	1.10	0.00000560	675
Loss of Function	1.21	10	15.1	0.663	7.09e-7	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000238
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000179	0.000176
Middle Eastern	0.000218	0.000217
South Asian	0.0000982	0.0000653
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as an adapter protein. {ECO:0000250}.

Recessive Scores

• pRec: 0.253

Intolerance Scores

• loftool: 0.552
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.74

Haploinsufficiency Scores

• pHI: 0.239
• hipred: N
• hipred_score: 0.207
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.616

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Shd

Gene ontology

• Molecular function: phosphotyrosine residue binding;protein binding