PRH1

proline rich protein HaeIII subfamily 1, the group of Proline rich proteins

Basic information

Region (hg38): 12:10824959-11171608

Links

ENSG00000231887 ∙ NCBI:5554 ∙ OMIM:168730 ∙ HGNC:9366 ∙ Uniprot:P02810 ∙ 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 PRH1 gene.

• Inborn genetic diseases (6 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRH1 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			5	2	2	9
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	3	2

Variants in PRH1

This is a list of pathogenic ClinVar variants found in the PRH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-10825426-T-A		not specified	Uncertain significance (Nov 08, 2021)
12-10825578-G-T		not specified	Uncertain significance (Feb 21, 2024)
12-10825616-G-C		not specified	Uncertain significance (Feb 27, 2024)
12-10825660-T-A		not specified	Uncertain significance (Jul 06, 2021)
12-10825677-A-G		not specified	Uncertain significance (Sep 01, 2021)
12-10825714-A-G		not specified	Uncertain significance (Mar 16, 2022)
12-10825728-C-G		not specified	Uncertain significance (Aug 12, 2021)
12-10825744-T-C		not specified	Likely benign (Dec 06, 2021)
12-10825837-C-G		not specified	Likely benign (Jul 15, 2021)
12-10825935-T-G		not specified	Uncertain significance (Dec 21, 2023)
12-10825977-A-G		not specified	Uncertain significance (Mar 05, 2024)
12-10826038-C-T		not specified	Uncertain significance (Feb 06, 2023)
12-10826061-A-G		not specified	Uncertain significance (Nov 15, 2021)
12-10826089-T-C		not specified	Uncertain significance (Nov 22, 2021)
12-10826103-A-T		not specified	Uncertain significance (Sep 22, 2021)
12-10826125-C-T		not specified	Uncertain significance (Feb 28, 2023)
12-10826185-G-C		not specified	Uncertain significance (Aug 09, 2021)
12-10826233-C-A		not specified	Uncertain significance (Jul 25, 2023)
12-10826257-C-T		not specified	Uncertain significance (Mar 14, 2023)
12-10826263-G-A		not specified	Uncertain significance (Apr 06, 2023)
12-10847042-T-G		PRR4-related disorder	Likely benign (Jun 21, 2019)
12-10847101-T-C		not specified	Uncertain significance (Jun 24, 2022)
12-10847109-T-C		PRR4-related disorder	Benign (Oct 17, 2019)
12-10847115-A-G		not specified	Uncertain significance (Aug 08, 2023)
12-10847154-G-T		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRH1	protein_coding	protein_coding	ENST00000428168	4	3245

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00722	0.783	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.694	72	90.6	0.795	0.00000442	1028
Missense in Polyphen		6	3.9748	1.5095		41
Synonymous	0.483	29	32.5	0.892	0.00000146	364
Loss of Function	0.955	4	6.66	0.601	2.85e-7	70

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

• Function: FUNCTION: PRP's act as highly potent inhibitors of crystal growth of calcium phosphates. They provide a protective and reparative environment for dental enamel which is important for the integrity of the teeth.
• Pathway: Salivary secretion - Homo sapiens (human) (Consensus)

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.255

Essentials

• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Gene ontology

• Cellular component: extracellular space
• Molecular function: protein binding