RSF1

Chr 11

remodeling and spacing factor 1

Also known as: HBXAP, RSF-1, XAP8, p325

NCBI Gene: 51773 ENSG00000048649 UniProt: Q96T23

This gene encodes a nuclear protein that interacts with hepatitis B virus X protein (HBX) and facilitates transcription of hepatitis B virus genes by the HBX transcription activator, suggesting a role for this interaction in the virus life cycle. This protein also interacts with SNF2H protein to form the RSF chromatin-remodeling complex, where the SNF2H subunit functions as the nucleosome-dependent ATPase, and this protein as the histone chaperone. [provided by RefSeq, Sep 2011]

Research

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

0.04

LOEUF· LoF intol.

LOF

Mechanism· predicted

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?

0.04LOEUF

pLI 1.000

Z-score 7.63

OE 0.00 (0.00–0.04)

Highly constrained

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

Missense Constraint?

1.77Z-score

OE missense 0.82 (0.77–0.88)

620 obs / 756.7 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.00 (0.00–0.04)

0≤0.351.4

Missense OE?0.82 (0.77–0.88)

0≤0.61.4

Synonymous OE?0.98

0≤1.21.6

LoF obs/exp: 0 / 67.8Missense obs/exp: 620 / 756.7Syn Z: 0.30

Background carrier burden — how many people carry a rare variant somewhere in RSF1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 42

1,615 rare PASS variants

Rare truncating (LoF)

1 in 9,800

29 rare PASS variants

Rare synonymous (reference)

1 in 96

609 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for RSF1. 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 52	1 in 12,000
South Asian	~43k	1 in 35	≈ 1 in 40,000
Remaining (unassigned)	~30k	1 in 39	≈ 1 in 7,200
European (Finnish)	~27k	1 in 130	1 in 5,300
Admixed American	~22k	1 in 35	1 in 3,900
African / African American	~21k	1 in 31	≈ 1 in 17,000
East Asian	~20k	1 in 46	≈ 1 in 4,800
Ashkenazi Jewish	~13k	1 in 190	≈ 1 in 6,400
Middle Eastern	~2,884	1 in 38	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): 12 of 16 coding exons well covered in gnomAD exomes; exons 2, 3, 10, 12 marginal. Genomes: all 16.? see exons ↓