SH2D5

SH2 domain containing 5

Basic information

Region (hg38): 1:20719730-20732837

Links

ENSG00000189410 ∙ NCBI:400745 ∙ ∙ HGNC:28819 ∙ Uniprot:Q6ZV89 ∙ 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 SH2D5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH2D5 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			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	1	0

Variants in SH2D5

This is a list of pathogenic ClinVar variants found in the SH2D5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-20721796-C-T		not specified	Uncertain significance (Sep 29, 2023)
1-20721818-C-T		not specified	Uncertain significance (Nov 09, 2022)
1-20721869-G-C		not specified	Uncertain significance (Nov 05, 2021)
1-20721947-C-T		not specified	Uncertain significance (Mar 25, 2022)
1-20721994-T-C		not specified	Uncertain significance (Nov 10, 2022)
1-20722769-C-T		not specified	Uncertain significance (Dec 07, 2021)
1-20722791-C-G		not specified	Uncertain significance (Jan 19, 2024)
1-20722800-G-A		not specified	Uncertain significance (Feb 06, 2024)
1-20722820-C-T		not specified	Likely benign (Aug 12, 2021)
1-20722874-G-A		not specified	Uncertain significance (Oct 05, 2023)
1-20723648-A-G		not specified	Uncertain significance (Apr 30, 2024)
1-20723708-G-A		not specified	Uncertain significance (Sep 14, 2022)
1-20723723-A-G		not specified	Uncertain significance (Feb 07, 2023)
1-20724097-G-A		not specified	Uncertain significance (Feb 23, 2023)
1-20724133-T-C		not specified	Uncertain significance (Sep 22, 2023)
1-20724142-G-A		not specified	Uncertain significance (May 20, 2024)
1-20724235-G-A		not specified	Uncertain significance (Dec 08, 2023)
1-20724428-G-A		not specified	Uncertain significance (Nov 07, 2022)
1-20724430-C-T		not specified	Uncertain significance (Nov 14, 2023)
1-20724439-A-G		not specified	Uncertain significance (May 24, 2023)
1-20724472-C-T		not specified	Uncertain significance (Mar 15, 2024)
1-20724488-G-A		not specified	Uncertain significance (Nov 05, 2021)
1-20724520-A-G		not specified	Uncertain significance (Feb 17, 2024)
1-20724563-C-A		not specified	Uncertain significance (Mar 18, 2024)
1-20724608-G-A		not specified	Uncertain significance (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH2D5	protein_coding	protein_coding	ENST00000444387	9	13106

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.45e-8	0.688	124650	1	94	124745	0.000381

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.682	240	272	0.884	0.0000184	2649
Missense in Polyphen		99	111.28	0.88968		1060
Synonymous	0.406	109	115	0.952	0.00000742	915
Loss of Function	1.25	14	20.0	0.700	0.00000100	207

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000282	0.000276
Ashkenazi Jewish	0.000100	0.0000994
East Asian	0.00	0.00
Finnish	0.00312	0.00307
European (Non-Finnish)	0.000158	0.000150
Middle Eastern	0.00	0.00
South Asian	0.000136	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in synaptic plasticity regulation through the control of Rac-GTP levels. {ECO:0000250|UniProtKB:Q8JZW5}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.269
• rvis_EVS: -0.38
• rvis_percentile_EVS: 28.01

Haploinsufficiency Scores

• pHI: 0.230
• hipred: N
• hipred_score: 0.373
• ghis: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.179

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh2d5
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Cellular component: postsynaptic density;cell junction;postsynaptic membrane