H1-10

Chr 3

H1.10 linker histone

Also known as: H1.10, H1FX, H1X

NCBI Gene: 8971 ENSG00000184897 UniProt: Q92522 OMIM: 602785

Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene encodes a replication-independent histone that is a member of the histone H1 family. [provided by RefSeq, Oct 2015]

OMIM Research

OMIM ResearchGenerating clinical summary…

LOFmechanismLOEUF 1.35

Clinical Summary— H1-10

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Population Constraint (gnomAD)

Low constraint (pLI 0.09) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

32 VUS of 32 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.35LOEUF

pLI 0.088

Z-score 1.11

OE 0.44 (0.18–1.35)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.46Z-score

OE missense 0.88 (0.75–1.04)

101 obs / 114.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.44 (0.18–1.35)

0≤0.351.4

Missense OE?0.88 (0.75–1.04)

0≤0.61.4

Synonymous OE?1.23

0≤1.21.6

LoF obs/exp: 2 / 4.5Missense obs/exp: 101 / 114.8Syn Z: -1.29

This gene — mechanism propensity

0.3196th %ile

GOF

0.3094th %ile

LOF

0.77top 5%

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

LOFprediction above median

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

32 submitted variants in ClinVar

ClinVar

Classification Summary

VUS32

VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	32	32
Likely Benign	0	0
Benign	0	0
Total	32	32

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

View in ClinVar →

9 pathogenic / likely-pathogenic (of 13) ClinVar copy-number / structural variants overlap H1-10 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →