RTF1

Chr 15

RTF1 homolog, Paf1/RNA polymerase II complex component

Also known as: GTL7, KIAA0252

NCBI Gene: 23168 ENSG00000137815 UniProt: Q92541 OMIM: 611633

This locus may represent a gene involved in regulation of transcription elongation and chromatin remodeling, based on studies of similar proteins in other organisms. The encoded protein may bind single-stranded DNA. [provided by RefSeq, Sep 2010]

OMIM Research

OMIM ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.12

LOEUF· LoF intol.

LOF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Dual constrained — LoF & missense intolerant

LoF Constraint?

0.12LOEUF

pLI 1.000

Z-score 5.64

OE 0.03 (0.01–0.12)

Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint?

4.59Z-score

OE missense 0.31 (0.27–0.36)

109 obs / 351.1 exp

Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?

LoF OE?0.03 (0.01–0.12)

0≤0.351.4

Missense OE?0.31 (0.27–0.36)

0≤0.61.4

Synonymous OE?0.95

0≤1.21.6

LoF obs/exp: 1 / 39.0Missense obs/exp: 109 / 351.1Syn Z: 0.43

Background carrier burden — how many people carry a rare variant somewhere in RTF1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 190

512 rare PASS variants

Rare truncating (LoF)

1 in 6,500

33 rare PASS variants

Rare synonymous (reference)

1 in 180

332 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for RTF1. 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)	~556k	1 in 190	1 in 6,000
South Asian	~43k	1 in 230	1 in 2,500
Remaining (unassigned)	~30k	1 in 210	none seen
European (Finnish)	~27k	1 in 350	none seen
Admixed American	~22k	1 in 160	≈ 1 in 22,000
African / African American	~21k	1 in 190	≈ 1 in 21,000
East Asian	~20k	1 in 230	≈ 1 in 5,700
Ashkenazi Jewish	~13k	1 in 400	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 160	none seen

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): 15 of 18 coding exons well covered in gnomAD exomes; exons 1, 6, 11 marginal. Genomes: all 18.? see exons ↓