SHF

Src homology 2 domain containing F, the group of SH2 domain containing

Basic information

Region (hg38): 15:45167214-45201175

Links

ENSG00000138606 ∙ NCBI:90525 ∙ OMIM:617313 ∙ HGNC:25116 ∙ Uniprot:Q7M4L6 ∙ 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 SHF gene.

• not_specified (39 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHF gene is commonly pathogenic or not. These statistics are base on transcript: NM_001394037.1. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			39			39
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	39	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHF	protein_coding	protein_coding	ENST00000290894	7	33962

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.160	0.839	125576	0	17	125593	0.0000677

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.866	211	250	0.846	0.0000137	2707
Missense in Polyphen		55	79.821	0.68904		868
Synonymous	0.803	91	101	0.898	0.00000553	861
Loss of Function	3.00	5	19.2	0.261	0.00000107	216

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000802	0.0000793
Middle Eastern	0.000164	0.000163
South Asian	0.0000681	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adapter protein which may play a role in the regulation of apoptosis in response to PDGF. {ECO:0000269|PubMed:11095946}.
• Pathway: PDGFR-alpha signaling pathway (Consensus)

Recessive Scores

• pRec: 0.144

Intolerance Scores

• loftool: 0.731
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.57

Haploinsufficiency Scores

• pHI: 0.194
• hipred: N
• hipred_score: 0.364
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.669

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Shf

Gene ontology

• Biological process: apoptotic process
• Molecular function: phosphotyrosine residue binding