SHF

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

Basic information

Region (hg38): 15:45167213-45201175

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.

• Inborn genetic diseases (14 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.

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			14			14
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	0	0

Variants in SHF

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

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

Position	Type	Phenotype	Significance	ClinVar
15-45168014-C-T		not specified	Uncertain significance (May 09, 2023)
15-45168017-C-T		not specified	Uncertain significance (Jan 22, 2024)
15-45168060-G-A		not specified	Uncertain significance (Jan 26, 2022)
15-45168078-C-G		not specified	Uncertain significance (Aug 10, 2021)
15-45172165-A-T		not specified	Uncertain significance (Nov 21, 2023)
15-45172252-G-A		not specified	Uncertain significance (Jul 14, 2021)
15-45172262-G-A		not specified	Uncertain significance (Jun 08, 2022)
15-45172277-G-A		not specified	Uncertain significance (Aug 02, 2021)
15-45172303-G-A		not specified	Uncertain significance (Apr 19, 2023)
15-45173716-A-G		not specified	Uncertain significance (Sep 09, 2021)
15-45175227-G-A		not specified	Uncertain significance (Jun 28, 2022)
15-45175239-C-T		not specified	Uncertain significance (Jun 11, 2021)
15-45175240-G-A		not specified	Uncertain significance (Feb 12, 2024)
15-45175284-C-A		not specified	Uncertain significance (Oct 18, 2021)
15-45175305-C-T		not specified	Uncertain significance (Nov 14, 2023)
15-45175315-G-C		not specified	Uncertain significance (Dec 15, 2023)
15-45175317-G-T		not specified	Uncertain significance (Apr 05, 2023)
15-45175341-G-A		not specified	Uncertain significance (Jan 16, 2024)
15-45178172-C-T		not specified	Uncertain significance (Nov 16, 2022)
15-45178211-T-A		not specified	Uncertain significance (Apr 06, 2023)
15-45178231-C-T		not specified	Uncertain significance (Apr 07, 2023)
15-45178271-A-T		not specified	Uncertain significance (Jan 02, 2024)
15-45178275-A-C		not specified	Uncertain significance (Nov 13, 2023)
15-45178275-A-G		not specified	Uncertain significance (Oct 27, 2021)
15-45198773-G-A		not specified	Uncertain significance (Feb 15, 2023)

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