NABP1

Chr 2

nucleic acid binding protein 1

Also known as: NABP1-OT1, OBFC2A, SOSS-B2, SSB2

NCBI Gene: 64859 ENSG00000173559 UniProt: Q96AH0 OMIM: 612103

NABP1 encodes a single-stranded DNA-binding protein that functions as a component of the SOSS complex, which is essential for DNA repair, homologous recombination, and cell-cycle checkpoint activation following DNA damage. The gene shows very low constraint against loss-of-function variants (pLI 0.00003, LOEUF 1.356), and currently no established Mendelian diseases have been linked to NABP1 mutations in the provided data.

OMIM ResearchSummary from RefSeq, UniProt

Single-stranded DNA (ssDNA)-binding proteins, such as OBFC2A, are ubiquitous and essential for a variety of DNA metabolic processes, including replication, recombination, and detection and repair of damage (Richard et al., 2008 [PubMed 18449195]).[supplied by OMIM, Jun 2008]

OMIM ResearchGenerating clinical summary…

DNmechanismLOEUF 1.36

Clinical Summary— NABP1

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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

27 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?

1.36LOEUF

pLI 0.000

Z-score 0.75

OE 0.75 (0.44–1.36)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.03Z-score

OE missense 0.99 (0.85–1.16)

110 obs / 110.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.75 (0.44–1.36)

0≤0.351.4

Missense OE?0.99 (0.85–1.16)

0≤0.61.4

Synonymous OE?0.66

0≤1.21.6

LoF obs/exp: 8 / 10.6Missense obs/exp: 110 / 110.9Syn Z: 1.67

This gene — mechanism propensity

0.7230th %ile

GOF

0.4085th %ile

LOF

0.4331th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

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

ClinVar Variant Classifications

35 submitted variants in ClinVar

ClinVar

Classification Summary

VUS27

Likely Benign1

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	27	27
Likely Benign	1	1
Benign	0	0
Total	28	28

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

View in ClinVar →

29 pathogenic / likely-pathogenic (of 32) ClinVar copy-number / structural variants overlap NABP1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →