PRH2

proline rich protein HaeIII subfamily 2, the group of Proline rich proteins

Basic information

Region (hg38): 12:10929236-10934845

Links

ENSG00000134551 ∙ NCBI:5555 ∙ OMIM:168790 ∙ HGNC:9367 ∙ 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 PRH2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRH2 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in PRH2

This is a list of pathogenic ClinVar variants found in the PRH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-10930302-C-T		not specified	Uncertain significance (Jul 09, 2021)
12-10930667-G-A		not specified	Uncertain significance (Dec 10, 2024)
12-10930715-G-C		not specified	Uncertain significance (Apr 29, 2024)
12-10930754-C-A		not specified	Uncertain significance (Jan 11, 2023)
12-10930773-A-G		not specified	Uncertain significance (Feb 28, 2024)
12-10930781-C-A		not specified	Uncertain significance (Apr 18, 2024)
12-10930809-G-A		not specified	Uncertain significance (Nov 03, 2022)
12-10930826-G-A		not specified	Uncertain significance (Dec 02, 2021)
12-10930836-A-G		not specified	Uncertain significance (Feb 14, 2024)
12-10930856-G-T		not specified	Uncertain significance (Sep 22, 2022)
12-10930859-C-A		not specified	Uncertain significance (Jan 08, 2024)
12-10930862-C-A		not specified	Uncertain significance (Feb 28, 2023)
12-10930917-G-C		not specified	Uncertain significance (Oct 12, 2021)
12-10930926-G-A		not specified	Uncertain significance (Jun 10, 2024)
12-10930983-C-T		not specified	Uncertain significance (Jul 11, 2023)
12-10931043-A-T		not specified	Uncertain significance (Feb 05, 2024)
12-10931054-C-T		not specified	Uncertain significance (Aug 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRH2	protein_coding	protein_coding	ENST00000396400	3	3106

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0125	0.668	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.640	72	89.0	0.809	0.00000438	1016
Missense in Polyphen		2	3.215	0.62207		37
Synonymous	0.485	28	31.5	0.890	0.00000145	361
Loss of Function	0.519	3	4.14	0.725	1.76e-7	50

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.000163	0.000163
South Asian	0.000131	0.000131
Other	0.000163	0.000163

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)

Intolerance Scores

• loftool: 0.947
• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.48

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.255
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.118

Gene Damage Prediction

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