SIRPB2

signal regulatory protein beta 2, the group of V-set domain containing|Signal regulatory proteins

Basic information

Region (hg38): 20:1470741-1491587

Previous symbols: [ "PTPN1L", "PTPNS1L3" ]

Links

ENSG00000196209 ∙ NCBI:284759 ∙ ∙ HGNC:16247 ∙ Uniprot:Q5JXA9 ∙ 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 SIRPB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIRPB2 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
missense			14	3		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	4	0

Variants in SIRPB2

This is a list of pathogenic ClinVar variants found in the SIRPB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-1476267-G-A		not specified	Uncertain significance (Feb 13, 2023)
20-1476288-G-A		not specified	Uncertain significance (Mar 24, 2023)
20-1476319-C-T		not specified	Likely benign (Dec 02, 2022)
20-1478344-T-C		not specified	Uncertain significance (Jul 12, 2023)
20-1478380-T-C		not specified	Uncertain significance (Jul 20, 2021)
20-1478407-C-T		not specified	Uncertain significance (Jul 20, 2022)
20-1478493-C-T		not specified	Uncertain significance (Mar 18, 2024)
20-1478504-G-A			Likely benign (Jan 01, 2023)
20-1478544-G-A		not specified	Uncertain significance (May 03, 2023)
20-1478599-C-A		not specified	Uncertain significance (Sep 15, 2021)
20-1478599-C-T		not specified	Uncertain significance (Apr 24, 2024)
20-1479729-G-A		not specified	Likely benign (Sep 17, 2021)
20-1479780-G-C		not specified	Uncertain significance (Aug 02, 2022)
20-1479814-A-G		not specified	Uncertain significance (Sep 06, 2022)
20-1479849-C-T		not specified	Uncertain significance (Feb 27, 2024)
20-1479868-C-T		not specified	Uncertain significance (Jul 19, 2023)
20-1479885-C-T		not specified	Likely benign (Feb 13, 2024)
20-1479886-G-A		not specified	Uncertain significance (Jul 09, 2021)
20-1479994-C-T		not specified	Uncertain significance (Aug 02, 2023)
20-1480029-A-G		not specified	Uncertain significance (Nov 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIRPB2	protein_coding	protein_coding	ENST00000359801	5	20848

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000366	0.848	124462	2	129	124593	0.000526

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.205	177	185	0.957	0.00000934	2204
Missense in Polyphen		68	61.022	1.1144		792
Synonymous	-0.0111	76	75.9	1.00	0.00000402	712
Loss of Function	1.27	7	11.7	0.598	4.99e-7	142

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000938	0.0000938
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000534	0.0000531
Middle Eastern	0.00	0.00
South Asian	0.00402	0.00396
Other	0.000332	0.000330

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0871

Intolerance Scores

• loftool: 0.851
• rvis_EVS: 1.02
• rvis_percentile_EVS: 90.92

Haploinsufficiency Scores

• pHI: 0.142
• hipred: N
• hipred_score: 0.148
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.141

Gene Damage Prediction

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

Gene ontology

• Cellular component: plasma membrane;integral component of membrane