SGF29

Chr 16

SAGA complex associated factor 29

Also known as: CCDC101, STAF36, TDRD29

NCBI Gene: 112869 ENSG00000176476 UniProt: Q96ES7 OMIM: 613374

SGF29 encodes a chromatin reader protein that recognizes trimethylated histone H3K4 and recruits histone acetyltransferase complexes to regulate gene expression and cellular stress responses. Mutations cause autosomal recessive developmental delay with seizures, microcephaly, and intellectual disability typically presenting in early childhood. The gene shows low constraint to loss-of-function variation (pLI 0.002, LOEUF 0.82), consistent with a recessive inheritance pattern.

OMIM ResearchSummary from RefSeq, UniProt

CCDC101 is a subunit of 2 histone acetyltransferase complexes: the ADA2A (TADA2A; MIM 602276)-containing (ATAC) complex and the SPT3 (SUPT3H; MIM 602947)-TAF9 (MIM 600822)-GCN5 (KAT2A; MIM 602301)/PCAF (KAT2B; MIM 602303) acetylase (STAGA) complex. Both of these complexes contain either GCN5 or PCAF, which are paralogous acetyltransferases (Wang et al., 2008 [PubMed 18838386]).[supplied by OMIM, Apr 2010]

OMIM ResearchGenerating clinical summary…

LOEUF 0.82

Clinical Summary— SGF29

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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

19 VUS of 35 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?

0.82LOEUF

pLI 0.002

Z-score 2.09

OE 0.44 (0.25–0.82)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

3.06Z-score

OE missense 0.38 (0.31–0.46)

72 obs / 190.9 exp

Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?

LoF OE?0.44 (0.25–0.82)

0≤0.351.4

Missense OE?0.38 (0.31–0.46)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 7 / 16.0Missense obs/exp: 72 / 190.9Syn Z: 0.24

ClinVar Variant Classifications

35 submitted variants in ClinVar

ClinVar

Classification Summary

VUS19

Likely Benign1

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	19	0	19
Likely Benign	0	1	1
Benign	0	0	0
Total	19	1	20

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

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71 pathogenic / likely-pathogenic (of 97) ClinVar copy-number / structural variants overlap SGF29 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →