PRMT7

Chr 16AR

protein arginine methyltransferase 7

Also known as: SBIDDS

NCBI Gene: 54496 ENSG00000132600 UniProt: Q9NVM4 OMIM: 610087

The protein arginine methyltransferase PRMT7 transfers methyl groups to arginine residues on histones and other proteins, mediating gene regulation, small nuclear ribonucleoprotein assembly, and genomic imprinting processes. Mutations cause syndromic intellectual disability with short stature and additional developmental features, inherited in an autosomal recessive pattern. This gene shows extremely high constraint against loss-of-function variants, indicating that complete loss of function is likely incompatible with survival.

OMIM ResearchSummary from RefSeq, UniProt

This gene encodes a member of the protein arginine N-methyltransferase family of proteins. The encoded enzyme transfers single methyl groups to arginine residues to generate monomethylarginines on histone proteins as well as other protein substrates. This enzyme plays a role in a wide range of biological processes, including neuronal differentiation, male germ line imprinting, small nuclear ribonucleoprotein biogenesis, and regulation of the Wnt signaling pathway. Mutations in this gene underlie multiple related syndromes in human patients characterized by intellectual disability, short stature and other features. The encoded protein may promote breast cancer cell invasion and metastasis in human patients. [provided by RefSeq, May 2017]

OMIM ResearchGenerating clinical summary…

LOFmechanismARLOEUF 0.991 OMIM phenotype

Clinical Summary— PRMT7

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

48 unique Pathogenic / Likely Pathogenic· 157 VUS of 374 total submissions

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Clinical Trials

1 active or recruiting trial — potential therapeutic options may be available

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.99LOEUF

pLI 0.000

Z-score 1.62

OE 0.72 (0.53–0.99)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.68Z-score

OE missense 0.91 (0.83–0.99)

386 obs / 425.6 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.72 (0.53–0.99)

0≤0.351.4

Missense OE?0.91 (0.83–0.99)

0≤0.61.4

Synonymous OE?1.07

0≤1.21.6

LoF obs/exp: 28 / 38.9Missense obs/exp: 386 / 425.6Syn Z: -0.73

ClinVar Variant Classifications

374 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic23

Likely Pathogenic25

VUS157

Likely Benign111

Benign19

Conflicting13

Pathogenic

Likely Pathogenic

157

VUS

111

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	20	1	2	0	23
Likely Pathogenic	17	7	1	0	25
VUS	1	145	10	1	157
Likely Benign	2	13	42	54	111
Benign	0	2	9	8	19
Conflicting	—				13
Total	40	168	64	63	348

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

22 pathogenic / likely-pathogenic (of 34) ClinVar copy-number / structural variants overlap PRMT7 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →