PHGR1

proline, histidine and glycine rich 1

Basic information

Region (hg38): 15:40351033-40356434

Links

ENSG00000233041 ∙ NCBI:644844 ∙ ∙ HGNC:37226 ∙ Uniprot:C9JFL3 ∙ 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 PHGR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHGR1 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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	3	0

Variants in PHGR1

This is a list of pathogenic ClinVar variants found in the PHGR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-40356088-G-T		not specified	Uncertain significance (Jul 26, 2021)
15-40356118-G-A		not specified	Uncertain significance (Oct 24, 2024)
15-40356124-C-A		not specified	Uncertain significance (Jul 30, 2024)
15-40356133-C-T		not specified	Uncertain significance (Dec 10, 2024)
15-40356157-C-A		not specified	Uncertain significance (Mar 16, 2024)
15-40356163-C-G		not specified	Uncertain significance (Nov 07, 2024)
15-40356164-A-G		not specified	Uncertain significance (Nov 07, 2024)
15-40356167-A-G		not specified	Uncertain significance (Apr 27, 2024)
15-40356184-G-A			Likely benign (Apr 01, 2022)
15-40356189-A-T			Likely benign (Jul 01, 2022)
15-40356195-T-A			Likely benign (Aug 01, 2024)
15-40356229-C-G		not specified	Uncertain significance (Jul 16, 2024)
15-40356245-C-G		not specified	Uncertain significance (Jan 18, 2025)
15-40356272-C-T		not specified	Uncertain significance (Jan 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHGR1	protein_coding	protein_coding	ENST00000448599	3	5402

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.142	0.642	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.736	33	47.2	0.699	0.00000245	517
Missense in Polyphen
Synonymous	1.13	13	19.3	0.672	0.00000122	178
Loss of Function	0.622	1	1.93	0.517	8.19e-8	23

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

Haploinsufficiency Scores

• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phgr1