SHOC1

Chr 9AR

shortage in chiasmata 1

Also known as: C9orf84, MZIP2, SPGF75, ZIP2, ZIP2H

NCBI Gene: 158401ENSG00000165181UniProt: Q5VXU9OMIM: 618038

The SHOC1 protein is an ATPase that binds single-stranded DNA and is essential for meiotic recombination, synaptonemal complex assembly, and homologous chromosome pairing during germ cell development. Biallelic mutations cause spermatogenic failure 75, a form of male infertility following autosomal recessive inheritance. The gene shows very low constraint against loss-of-function variants (pLI near zero), consistent with its recessive inheritance pattern and reproductive-specific phenotype.

OMIMResearchSummary from RefSeq, OMIM, UniProt
ARLOEUF 0.851 OMIM phenotype
Clinical Summary— SHOC1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
45 unique Pathogenic / Likely Pathogenic· 17 VUS of 86 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.85LOEUF
pLI 0.000
Z-score 2.60
OE 0.66 (0.52–0.85)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
1.32Z-score
OE missense 0.86 (0.80–0.92)
582 obs / 679.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.66 (0.52–0.85)
0≤0.351.4
Missense OE0.86 (0.80–0.92)
0≤0.61.4
Synonymous OE0.81
0≤1.21.6
LoF obs/exp: 45 / 68.2Missense obs/exp: 582 / 679.0Syn Z: 2.35

ClinVar Variant Classifications

86 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic39
Likely Pathogenic6
VUS17
Likely Benign6
39
Pathogenic
6
Likely Pathogenic
17
VUS
6
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
9
2
28
0
39
Likely Pathogenic
2
0
4
0
6
VUS
0
13
4
0
17
Likely Benign
0
2
0
4
6
Benign
0
0
0
0
0
Total111736468

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

View in ClinVar →

Protein Context — Lollipop Plot

SHOC1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients