AHCTF1

Chr 1

AT-hook containing transcription factor 1

Also known as: ELYS, MST108, MSTP108, TMBS62

NCBI Gene: 25909 ENSG00000153207 UniProt: Q8WYP5

The protein is required for nuclear pore complex assembly and completion of cytokinesis by binding to chromatin and recruiting nuclear pore subcomplexes. Mutations cause autosomal dominant neurodevelopmental disorder with language impairment and behavioral abnormalities. This gene is extremely intolerant to loss-of-function variants, indicating that even heterozygous disruption can cause disease.

ResearchSummary from RefSeq, UniProt

Predicted to enable DNA binding activity. Involved in nuclear pore complex assembly and regulation of cytokinesis. Located in chromosome; nuclear body; and nuclear envelope. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.13

Clinical Summary— AHCTF1

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.

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ClinVar Variants

281 VUS of 358 total submissions

Explore recent and relevant literature in Research Assistant →

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.13LOEUF

pLI 1.000

Z-score 9.11

OE 0.07 (0.04–0.13)

Highly constrained

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

Missense Constraint?

-0.38Z-score

OE missense 1.03 (0.98–1.08)

1176 obs / 1139.8 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.07 (0.04–0.13)

0≤0.351.4

Missense OE?1.03 (0.98–1.08)

0≤0.61.4

Synonymous OE?1.01

0≤1.21.6

LoF obs/exp: 8 / 112.1Missense obs/exp: 1176 / 1139.8Syn Z: -0.12

This gene — mechanism propensity

0.2599th %ile

GOF

0.14100th %ile

LOF

0.83top 5%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.13

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

358 submitted variants in ClinVar

ClinVar

Classification Summary

VUS281

Likely Benign29

281

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0	0
Likely Pathogenic	0	0	0	0
VUS	1	280	0	281
Likely Benign	0	25	4	29
Benign	0	0	0	0
Total	1	305	4	310

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

View in ClinVar →

75 pathogenic / likely-pathogenic (of 99) ClinVar copy-number / structural variants overlap AHCTF1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →