SASH3

SAM and SH3 domain containing 3, the group of SAM and SH3 domain containing|Sterile alpha motif domain containing

Basic information

Region (hg38): X:129779949-129795201

Previous symbols: [ "CXorf9" ]

Links

ENSG00000122122 ∙ NCBI:54440 ∙ OMIM:300441 ∙ HGNC:15975 ∙ Uniprot:O75995 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• immunodeficiency 102 (Strong), mode of inheritance: XL
• combined immunodeficiency, X-linked (Strong), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency 102	XL	Allergy/Immunology/Infectious	The condition can involve immunodeficiencies as well as immune dysregulation, and prophylaxis and early and aggressive treatment of infections may be beneficial	Allergy/Immunology/Infectious; Hematologic	33876203; 35464398

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SASH3 gene.

• Immunodeficiency 102 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SASH3 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				2		2
missense			29	1	1	31
nonsense	1					1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding					2	2
Total	1	0	30	3	3

Variants in SASH3

This is a list of pathogenic ClinVar variants found in the SASH3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-129788035-G-A		not specified	Uncertain significance (Dec 02, 2022)
X-129788059-C-A		not specified	Uncertain significance (Oct 12, 2024)
X-129788442-T-C			Likely benign (Jan 01, 2023)
X-129788529-G-A		not specified	Uncertain significance (Jan 23, 2024)
X-129788554-G-A		not specified	Uncertain significance (Nov 09, 2022)
X-129790968-C-G		Immunodeficiency 102	Uncertain significance (-)
X-129791019-C-T		not specified	Uncertain significance (Mar 01, 2024)
X-129791039-G-A		not specified	Uncertain significance (Oct 07, 2024)
X-129791067-G-A		not specified	Uncertain significance (Mar 31, 2024)
X-129791084-G-A		Immunodeficiency	Uncertain significance (Feb 02, 2022)
X-129791180-T-G		not specified	Benign (Jan 24, 2024)
X-129792351-C-T		not specified	Uncertain significance (Sep 28, 2022)
X-129792369-G-A		not specified	Uncertain significance (Mar 06, 2023)
X-129792385-C-A		not specified	Uncertain significance (Mar 19, 2024)
X-129792390-C-T		Immunodeficiency 102	Pathogenic (May 31, 2022)
X-129792415-G-A		not specified	Uncertain significance (Jun 18, 2024)
X-129792432-G-A		not specified	Uncertain significance (Jul 05, 2023)
X-129792451-A-C			Uncertain significance (Apr 26, 2024)
X-129792463-C-T		not specified	Uncertain significance (Nov 13, 2024)
X-129792630-G-A		not specified	Uncertain significance (Apr 15, 2024)
X-129792738-G-A		not specified	Uncertain significance (Apr 26, 2023)
X-129792744-G-A		not specified	Uncertain significance (Dec 16, 2022)
X-129792747-G-C		not specified	Uncertain significance (May 26, 2023)
X-129792765-C-T			Benign (Jul 31, 2018)
X-129792766-G-A		not specified	Uncertain significance (Jan 29, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SASH3	protein_coding	protein_coding	ENST00000356892	8	15223

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.385	0.613	125715	1	2	125718	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.85	98	165	0.595	0.0000138	2483
Missense in Polyphen		17	59.636	0.28506		917
Synonymous	-1.30	88	73.8	1.19	0.00000660	773
Loss of Function	2.65	3	13.5	0.222	0.00000124	192

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000152	0.0000993
East Asian	0.00	0.00
Finnish	0.0000625	0.0000462
European (Non-Finnish)	0.0000122	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as a signaling adapter protein in lymphocytes. {ECO:0000250}.

Recessive Scores

• pRec: 0.263

Intolerance Scores

• loftool: 0.0772
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.19

Haploinsufficiency Scores

• pHI: 0.359
• hipred: Y
• hipred_score: 0.580
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.227

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sash3
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: positive regulation of immunoglobulin production;positive regulation of T cell cytokine production;positive regulation of adaptive immune response;positive regulation of B cell proliferation;positive regulation of interferon-gamma production;positive regulation of interleukin-10 production;positive regulation of interleukin-2 production;positive regulation of interleukin-4 production;positive regulation of tumor necrosis factor production;positive regulation of T cell proliferation;positive regulation of CD4-positive, alpha-beta T cell differentiation;positive regulation of organ growth;homeostasis of number of cells within a tissue
• Cellular component: nucleus;cytoplasm