ELF1

Chr 13

E74 like ETS transcription factor 1

Also known as: EFTUD1, RIA1

NCBI Gene: 1997 ENSG00000120690 UniProt: P32519

ELF1 encodes a transcription factor that regulates gene expression in lymphoid cells and activates specific promoters including LYN and BLK. Mutations cause autosomal dominant immunodeficiency with developmental delay and hypotonia, affecting both immune function and neurological development. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.58).

ResearchSummary from RefSeq, UniProt

This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2009]

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

0.58

LOEUF

—

Mechanism

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.58LOEUF

pLI 0.011

Z-score 3.12

OE 0.32 (0.19–0.58)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

0.91Z-score

OE missense 0.86 (0.78–0.95)

279 obs / 325.4 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.32 (0.19–0.58)

0≤0.351.4

Missense OE?0.86 (0.78–0.95)

0≤0.61.4

Synonymous OE?0.95

0≤1.21.6

LoF obs/exp: 8 / 24.7Missense obs/exp: 279 / 325.4Syn Z: 0.47

Background carrier burden — how many people carry a rare variant somewhere in ELF1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 94

677 rare PASS variants

Rare truncating (LoF)

1 in 3,900

61 rare PASS variants

Rare synonymous (reference)

1 in 150

270 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for ELF1. 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 130	1 in 2,900
South Asian	~43k	1 in 67	1 in 6,100
Remaining (unassigned)	~30k	1 in 77	none seen
European (Finnish)	~27k	1 in 240	≈ 1 in 13,000
Admixed American	~22k	1 in 59	none seen
African / African American	~21k	1 in 86	≈ 1 in 4,600
East Asian	~20k	1 in 93	1 in 3,300
Ashkenazi Jewish	~13k	1 in 390	none seen
Middle Eastern	~2,884	1 in 140	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): All 8 coding exons well covered in gnomAD exomes and genomes.? see exons ↓