SHPRH

SNF2 histone linker PHD RING helicase, the group of PHD finger proteins|Ring finger proteins

Basic information

Region (hg38): 6:145864244-145964423

Links

ENSG00000146414 ∙ NCBI:257218 ∙ OMIM:608048 ∙ HGNC:19336 ∙ Uniprot:Q149N8 ∙ 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 SHPRH gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHPRH 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			71	3	1	75
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					1	1
Total	0	0	71	5	2

Variants in SHPRH

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

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

Position	Type	Phenotype	Significance	ClinVar
6-145886771-C-A		not specified	Uncertain significance (May 16, 2024)
6-145886782-G-A		not specified	Uncertain significance (Apr 26, 2024)
6-145888033-T-C		not specified	Uncertain significance (Aug 12, 2021)
6-145888062-A-G		not specified	Uncertain significance (Mar 18, 2024)
6-145910521-G-A		not specified	Uncertain significance (Mar 19, 2024)
6-145910543-T-C		not specified	Uncertain significance (Dec 27, 2023)
6-145910588-T-C		not specified	Uncertain significance (Nov 13, 2023)
6-145913486-C-T		not specified	Uncertain significance (Jan 30, 2024)
6-145919374-C-G		not specified	Uncertain significance (Feb 03, 2022)
6-145919449-C-T		not specified	Uncertain significance (Apr 26, 2023)
6-145919501-T-C			Benign (Jun 27, 2018)
6-145921242-A-T		not specified	Uncertain significance (Sep 28, 2022)
6-145921319-T-C		not specified	Uncertain significance (Jul 14, 2021)
6-145922292-G-A		not specified	Uncertain significance (Nov 17, 2023)
6-145922812-C-A		not specified	Uncertain significance (Mar 27, 2023)
6-145922843-C-G			Likely benign (Jun 27, 2018)
6-145923700-C-T		not specified	Uncertain significance (Nov 16, 2021)
6-145923763-C-A		not specified	Uncertain significance (May 03, 2023)
6-145924809-T-C		not specified	Uncertain significance (Aug 21, 2023)
6-145924812-C-T		not specified	Uncertain significance (May 29, 2024)
6-145924828-G-C		not specified	Uncertain significance (Sep 12, 2023)
6-145924833-C-T		not specified	Uncertain significance (Oct 11, 2023)
6-145927271-T-C		not specified	Uncertain significance (Jan 06, 2023)
6-145934999-A-G			Likely benign (Jul 03, 2018)
6-145935048-C-T		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHPRH	protein_coding	protein_coding	ENST00000367505	29	100179

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000170	1.00	124734	1	61	124796	0.000248

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.33	694	889	0.780	0.0000461	11082
Missense in Polyphen		138	285.05	0.48413		3443
Synonymous	-0.520	320	308	1.04	0.0000156	3138
Loss of Function	6.21	29	93.9	0.309	0.00000559	1076

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000804	0.000802
Ashkenazi Jewish	0.000101	0.0000993
East Asian	0.000112	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000268	0.000265
Middle Eastern	0.000112	0.000111
South Asian	0.000343	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase involved in DNA repair. Upon genotoxic stress, accepts ubiquitin from the UBE2N-UBE2V2 E2 complex and transfers it to 'Lys-164' of PCNA which had been monoubiquitinated by UBE2A/B-RAD18, promoting the formation of non-canonical poly-ubiquitin chains linked through 'Lys-63'. {ECO:0000269|PubMed:17108083, ECO:0000269|PubMed:17130289, ECO:0000269|PubMed:18719106}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Protein ubiquitination;E3 ubiquitin ligases ubiquitinate target proteins (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.266
• rvis_EVS: -1.06
• rvis_percentile_EVS: 7.58

Haploinsufficiency Scores

• pHI: 0.132
• hipred: Y
• hipred_score: 0.648
• ghis: 0.649

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.751

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Shprh

Gene ontology

• Biological process: protein polyubiquitination;DNA repair;nucleosome assembly;cellular response to DNA damage stimulus;protein ubiquitination
• Cellular component: nucleosome;nucleoplasm
• Molecular function: DNA binding;helicase activity;ubiquitin-protein transferase activity;protein binding;ATP binding;ubiquitin protein ligase binding;metal ion binding;ubiquitin protein ligase activity