ELP2

Chr 18

elongator acetyltransferase complex subunit 2

Also known as: MRT58, SHINC-2, STATIP1, StIP

NCBI Gene: 55250 ENSG00000134759 UniProt: Q6IA86

ELP2 encodes a core subunit of the elongator complex, which catalyzes essential tRNA modifications including carboxymethyluridine formation at the wobble base position and functions as a histone acetyltransferase that associates with RNA polymerase II for transcriptional elongation. Biallelic mutations cause autosomal recessive intellectual developmental disorder. This represents a relatively recently described cause of intellectual disability involving defects in tRNA modification pathways.

GeneReviews ResearchSummary from RefSeq, OMIM, UniProt

The protein encoded by this gene is a core subunit of the elongator complex, a histone acetyltransferase complex that associates with RNA polymerase II. In addition to histone acetylation, the encoded protein effects transcriptional elongation and may help remodel chromatin. [provided by RefSeq, May 2016]

GeneReviews ResearchGenerating clinical summary…

LOEUF 0.88

Clinical Summary— ELP2

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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

18 unique Pathogenic / Likely Pathogenic· 157 VUS of 253 total submissions

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GeneReview available — ELP2

Authoritative clinical overview · Recommended first read

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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.88LOEUF

pLI 0.000

Z-score 2.30

OE 0.68 (0.53–0.88)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.58Z-score

OE missense 0.92 (0.85–1.00)

419 obs / 453.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.68 (0.53–0.88)

0≤0.351.4

Missense OE?0.92 (0.85–1.00)

0≤0.61.4

Synonymous OE?1.00

0≤1.21.6

LoF obs/exp: 40 / 59.1Missense obs/exp: 419 / 453.5Syn Z: 0.02

ClinVar Variant Classifications

253 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic4

Likely Pathogenic14

VUS157

Likely Benign37

Benign7

Conflicting6

Pathogenic

Likely Pathogenic

157

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	2	2	0	0	4
Likely Pathogenic	11	3	0	0	14
VUS	5	146	5	1	157
Likely Benign	0	13	2	22	37
Benign	0	3	1	3	7
Conflicting	—				6
Total	18	167	8	26	225

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

View in ClinVar →

47 pathogenic / likely-pathogenic (of 57) ClinVar copy-number / structural variants overlap ELP2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →