SIRPD

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

Basic information

Region (hg38): 20:1534250-1557705

Previous symbols: [ "PTPNS1L2" ]

Links

ENSG00000125900 ∙ NCBI:128646 ∙ ∙ HGNC:16248 ∙ Uniprot:Q9H106 ∙ 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 SIRPD gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

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

Variants in SIRPD

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

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

Position	Type	Phenotype	Significance	ClinVar
20-1537194-C-T		not specified	Likely benign (Feb 17, 2024)
20-1537211-T-C		not specified	Uncertain significance (Jul 05, 2022)
20-1551714-C-T		not specified	Likely benign (Feb 17, 2024)
20-1551715-G-A		not specified	Uncertain significance (Jul 06, 2022)
20-1551760-C-T		not specified	Uncertain significance (Sep 22, 2023)
20-1551799-G-A		not specified	Uncertain significance (Dec 28, 2023)
20-1551804-C-T		not specified	Uncertain significance (Nov 19, 2022)
20-1551805-G-A		not specified	Uncertain significance (Feb 06, 2023)
20-1551906-C-T		not specified	Uncertain significance (Aug 10, 2021)
20-1551960-C-T		not specified	Uncertain significance (Nov 13, 2023)
20-1557629-G-T		not specified	Uncertain significance (Jan 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIRPD	protein_coding	protein_coding	ENST00000381623	4	24593

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.91e-8	0.0585	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.884	136	110	1.24	0.00000598	1243
Missense in Polyphen		38	27.632	1.3752		346
Synonymous	-0.638	48	42.7	1.12	0.00000224	408
Loss of Function	-0.795	10	7.63	1.31	3.20e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.783
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• pHI: 0.0724
• hipred: N
• hipred_score: 0.112
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00741

Gene Damage Prediction

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

Gene ontology

• Cellular component: extracellular region;plasma membrane