PHGR1

Chr 15

proline, histidine and glycine rich 1

NCBI Gene: 644844 ENSG00000233041 UniProt: C9JFL3 OMIM: 621319

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.76

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.76LOEUF

pLI 0.142

Z-score 0.62

OE 0.52 (0.17–1.76)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.74Z-score

OE missense 0.70 (0.53–0.93)

33 obs / 47.2 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.52 (0.17–1.76)

0≤0.351.4

Missense OE?0.70 (0.53–0.93)

0≤0.61.4

Synonymous OE?0.67

0≤1.21.6

LoF obs/exp: 1 / 1.9Missense obs/exp: 33 / 47.2Syn Z: 1.13

Background carrier burden — how many people carry a rare variant somewhere in PHGR1?

gnomAD v4 · ~700k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 420

98 rare PASS variants

Rare truncating (LoF)

1 in 4,400

31 rare PASS variants

Rare synonymous (reference)

1 in 700

40 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for PHGR1. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~539k	1 in 470	1 in 5,500
South Asian	~40k	1 in 150	≈ 1 in 13,000
Remaining (unassigned)	~29k	1 in 290	≈ 1 in 8,600
European (Finnish)	~25k	1 in 400	1 in 630
African / African American	~21k	1 in 230	1 in 3,100
East Asian	~18k	1 in 770	1 in 1,600
Admixed American	~18k	1 in 380	≈ 1 in 8,600
Ashkenazi Jewish	~13k	1 in 1,100	none seen
Middle Eastern	~2,849	1 in 450	≈ 1 in 2,600

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 3 of 3 coding exons well covered in gnomAD exomes. Genomes: 2 of 3 (exon 4 below).? see exons ↓