CSRNP3

Chr 2

cysteine and serine rich nuclear protein 3

Also known as: FAM130A2, MBU1, PPP1R73, TAIP-2, TAIP2

NCBI Gene: 80034 ENSG00000178662 UniProt: Q8WYN3 OMIM: 620405

CSRNP3 encodes a transcriptional activator that binds specific DNA sequences and promotes apoptosis. Mutations cause autosomal recessive neurodevelopmental disorders with intellectual disability, seizures, and brain malformations. The gene shows high constraint against loss-of-function variants (LOEUF 0.445), indicating intolerance to inactivating mutations.

OMIM ResearchSummary from RefSeq, UniProt

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and sequence-specific DNA binding activity. Predicted to be involved in positive regulation of apoptotic process and positive regulation of transcription by RNA polymerase II. Predicted to be located in chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

LOEUF 0.45

Clinical Summary— CSRNP3

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Population Constraint (gnomAD)

Moderately constrained gene (pLI 0.50) — some intolerance to loss-of-function variants.

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ClinVar Variants

1 unique Pathogenic / Likely Pathogenic· 71 VUS of 79 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.45LOEUF

pLI 0.500

Z-score 3.55

OE 0.21 (0.11–0.45)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

1.59Z-score

OE missense 0.75 (0.68–0.84)

248 obs / 329.1 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.21 (0.11–0.45)

0≤0.351.4

Missense OE?0.75 (0.68–0.84)

0≤0.61.4

Synonymous OE?1.03

0≤1.21.6

LoF obs/exp: 5 / 23.6Missense obs/exp: 248 / 329.1Syn Z: -0.23

ClinVar Variant Classifications

79 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic1

VUS71

Likely Benign2

Benign2

Pathogenic

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	1	0	1
Likely Pathogenic	0	0	0	0
VUS	71	0	0	71
Likely Benign	1	0	1	2
Benign	0	0	2	2
Total	72	1	3	76

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

View in ClinVar →

50 pathogenic / likely-pathogenic (of 66) ClinVar copy-number / structural variants overlap CSRNP3 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →