SH2D3C

SH2 domain containing 3C, the group of SH2 domain containing|NSP adaptor proteins

Basic information

Region (hg38): 9:127738316-127778710

Links

ENSG00000095370 ∙ NCBI:10044 ∙ OMIM:604722 ∙ HGNC:16884 ∙ Uniprot:Q8N5H7 ∙ 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 SH2D3C gene.

• Inborn genetic diseases (34 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH2D3C 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	2
missense			31	4		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	5	1

Variants in SH2D3C

This is a list of pathogenic ClinVar variants found in the SH2D3C region.

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

Position	Type	Phenotype	Significance	ClinVar
9-127738822-C-T		not specified	Uncertain significance (Mar 13, 2023)
9-127738823-G-A		not specified	Uncertain significance (Sep 26, 2023)
9-127738832-G-T		not specified	Uncertain significance (Jun 11, 2021)
9-127741876-T-C		not specified	Uncertain significance (Dec 03, 2021)
9-127741889-C-T		not specified	Uncertain significance (Aug 23, 2021)
9-127741922-G-C		not specified	Uncertain significance (Jun 22, 2021)
9-127741928-C-T		not specified	Uncertain significance (Mar 07, 2023)
9-127741938-C-A		not specified	Uncertain significance (May 09, 2022)
9-127742904-T-C		not specified	Uncertain significance (Dec 15, 2022)
9-127742930-T-C		not specified	Uncertain significance (Nov 22, 2023)
9-127742943-T-C		not specified	Uncertain significance (Mar 29, 2023)
9-127742953-T-C		not specified	Uncertain significance (Sep 28, 2022)
9-127744602-G-A		not specified	Uncertain significance (Sep 06, 2022)
9-127744627-C-T			Benign (Jan 23, 2018)
9-127744638-G-A		not specified	Uncertain significance (Feb 12, 2024)
9-127744662-G-A		not specified	Uncertain significance (Jun 24, 2022)
9-127744725-C-T		not specified	Uncertain significance (Mar 03, 2022)
9-127744742-G-A		not specified	Uncertain significance (Oct 27, 2022)
9-127744847-C-T		not specified	Uncertain significance (Apr 26, 2023)
9-127744853-C-A		not specified	Uncertain significance (May 31, 2023)
9-127744860-C-T		not specified	Uncertain significance (Aug 17, 2021)
9-127744868-T-A		not specified	Uncertain significance (Dec 20, 2023)
9-127744911-T-C		not specified	Uncertain significance (Oct 05, 2023)
9-127744962-G-A		not specified	Likely benign (Jun 28, 2023)
9-127745037-C-A		not specified	Uncertain significance (Apr 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH2D3C	protein_coding	protein_coding	ENST00000314830	12	40425

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000351	1.00	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.95	415	543	0.765	0.0000345	5543
Missense in Polyphen		155	247.48	0.62631		2494
Synonymous	0.514	215	225	0.956	0.0000145	1803
Loss of Function	3.41	12	33.2	0.362	0.00000177	383

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000493	0.000246
Ashkenazi Jewish	0.000104	0.0000992
East Asian	0.000490	0.000489
Finnish	0.00	0.00
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.000490	0.000489
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Eph receptor-binding protein which may be a positive regulator of TCR signaling. Binding to BCAR1 is required to induce membrane ruffling and promote EGF-dependent cell migration (By similarity). {ECO:0000250}.
• Pathway: TCR (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.757
• rvis_EVS: -0.64
• rvis_percentile_EVS: 16.71

Haploinsufficiency Scores

• pHI: 0.337
• hipred: Y
• hipred_score: 0.709
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.911

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh2d3c
• Phenotype: immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: JNK cascade;small GTPase mediated signal transduction;positive regulation of signal transduction;positive regulation of peptidyl-serine phosphorylation
• Cellular component: cytoplasm;membrane
• Molecular function: SH3/SH2 adaptor activity;guanyl-nucleotide exchange factor activity;protein binding